6TH6 | pdb_00006th6

Cryo-EM Structure of T. kodakarensis 70S ribosome

PDB DOI: https://doi.org/10.2210/pdb6TH6/pdb
EM Map EMD-10503: EMDB EMDataResource
NAKB: 6TH6

Classification: RIBOSOME
Organism(s): Thermococcus kodakarensis KOD1
Mutation(s): No

Deposited: 2019-11-18 Released: 2020-07-29
Deposition Author(s): Matzov, D., Sas-Chen, A., Thomas, J.M., Santangelo, T., Meier, J.L., Schwartz, S., Shalev-Benami, M.

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.55 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.2 of the entry. See complete history.

Literature

Dynamic RNA acetylation revealed by quantitative cross-evolutionary mapping.

Sas-Chen, A., Thomas, J.M., Matzov, D., Taoka, M., Nance, K.D., Nir, R., Bryson, K.M., Shachar, R., Liman, G.L.S., Burkhart, B.W., Gamage, S.T., Nobe, Y., Briney, C.A., Levy, M.J., Fuchs, R.T., Robb, G.B., Hartmann, J., Sharma, S., Lin, Q., Florens, L., Washburn, M.P., Isobe, T., Santangelo, T.J., Shalev-Benami, M., Meier, J.L., Schwartz, S.

(2020) Nature 583: 638-643

PubMed: 32555463 Search on PubMed Search on PubMed Central
DOI: https://doi.org/10.1038/s41586-020-2418-2
Primary Citation Related Structures:
6SKF, 6SKG, 6TH6

PubMed Abstract:
N ⁴-acetylcytidine (ac ⁴C) is an ancient and highly conserved RNA modification that is present on tRNA and rRNA and has recently been investigated in eukaryotic mRNA ^1-3. However, the distribution, dynamics and functions of cytidine acetylation have yet to be fully elucidated. Here we report ac ⁴C-seq, a chemical genomic method for the transcriptome-wide quantitative mapping of ac ⁴C at single-nucleotide resolution. In human and yeast mRNAs, ac ⁴C sites are not detected but can be induced-at a conserved sequence motif-via the ectopic overexpression of eukaryotic acetyltransferase complexes. By contrast, cross-evolutionary profiling revealed unprecedented levels of ac ⁴C across hundreds of residues in rRNA, tRNA, non-coding RNA and mRNA from hyperthermophilic archaea. Ac ⁴C is markedly induced in response to increases in temperature, and acetyltransferase-deficient archaeal strains exhibit temperature-dependent growth defects. Visualization of wild-type and acetyltransferase-deficient archaeal ribosomes by cryo-electron microscopy provided structural insights into the temperature-dependent distribution of ac ⁴C and its potential thermoadaptive role. Our studies quantitatively define the ac ⁴C landscape, providing a technical and conceptual foundation for elucidating the role of this modification in biology and disease ^4-6.

Organizational Affiliation

Department of Molecular Genetics, Weizmann Institute of Science, Rehovot, Israel.

Macromolecule Content

Total Structure Weight: 2,430.84 kDa
Atom Count: 161,508
Modeled Residue Count: 12,264
Deposited Residue Count: 12,681
Unique protein chains: 58
Unique nucleic acid chains: 3

Macromolecules

Find similar proteins by:

| 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S2	B [auth Ab]	201	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJD2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJD2 Go to UniProtKB: Q5JJD2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJD2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3	C [auth Ac]	209	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JDH5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDH5 Go to UniProtKB: Q5JDH5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JDH5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 4
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S3Ae	D [auth Ad]	200	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JGM4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JGM4 Go to UniProtKB: Q5JGM4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JGM4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 5
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4	E [auth Ae]	180	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJF2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJF2 Go to UniProtKB: Q5JJF2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJF2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 6
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S4e	F [auth Af]	243	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJG0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJG0 Go to UniProtKB: Q5JJG0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJG0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 7
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S5	G [auth Ag]	235	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJG8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJG8 Go to UniProtKB: Q5JJG8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJG8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 8
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S6e	H [auth Ah]	125	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JDK8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDK8 Go to UniProtKB: Q5JDK8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JDK8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 9
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S7	I [auth Ai]	215	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JE04 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JE04 Go to UniProtKB: Q5JE04
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JE04
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 10
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8	J [auth Aj]	130	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJG3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJG3 Go to UniProtKB: Q5JJG3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJG3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 11
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S8e	K [auth Ak]	130	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JGF3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JGF3 Go to UniProtKB: Q5JGF3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JGF3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 12
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S9	L [auth Al]	135	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJE2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJE2 Go to UniProtKB: Q5JJE2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJE2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 13
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S10	M [auth Am]	102	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JFZ5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JFZ5 Go to UniProtKB: Q5JFZ5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JFZ5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 14
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S11	N [auth An]	140	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJF3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJF3 Go to UniProtKB: Q5JJF3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJF3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 15
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S12	O [auth Ao]	147	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JE20 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JE20 Go to UniProtKB: Q5JE20
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JE20
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 16
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S13	P [auth Ap]	149	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJF1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJF1 Go to UniProtKB: Q5JJF1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJF1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 17
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S15	Q [auth Aq]	151	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JGJ4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JGJ4 Go to UniProtKB: Q5JGJ4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JGJ4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 18
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S14 type Z	R [auth Ar]	56	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJG2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJG2 Go to UniProtKB: Q5JJG2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJG2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 19
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17	S [auth As]	114	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JDH9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDH9 Go to UniProtKB: Q5JDH9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JDH9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 20
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S17e	T [auth At]	67	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JDC7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDC7 Go to UniProtKB: Q5JDC7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JDC7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 21
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19	U [auth Au]	133	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JDH3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDH3 Go to UniProtKB: Q5JDH3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JDH3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 22
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S19e	V [auth Av]	150	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JGN5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JGN5 Go to UniProtKB: Q5JGN5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JGN5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 23
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S24e	W [auth Aw]	98	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JIY8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JIY8 Go to UniProtKB: Q5JIY8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JIY8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 24
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S27e	X [auth Ax]	65	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JE50 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JE50 Go to UniProtKB: Q5JE50
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JE50
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 25
Molecule	Chains	Sequence Length	Organism	Details	Image
30S ribosomal protein S28e	Y [auth Ay]	70	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JGR4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JGR4 Go to UniProtKB: Q5JGR4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JGR4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 26
Molecule	Chains	Sequence Length	Organism	Details	Image
Predicted zinc-ribbon RNA-binding protein involved in translation	Z [auth Az]	62	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JFE2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JFE2 Go to UniProtKB: Q5JFE2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JFE2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 29
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L2	CA [auth BC]	239	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JDH2 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDH2 Go to UniProtKB: Q5JDH2
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JDH2
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 30
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L3	DA [auth BD]	346	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JDJ0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDJ0 Go to UniProtKB: Q5JDJ0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JDJ0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 31
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L4	EA [auth BE]	255	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JDI0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDI0 Go to UniProtKB: Q5JDI0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JDI0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 32
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L5	FA [auth BF]	183	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJG1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJG1 Go to UniProtKB: Q5JJG1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJG1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 33
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L6	GA [auth BG]	184	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJG4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJG4 Go to UniProtKB: Q5JJG4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJG4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 34
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L7Ae	HA [auth BH], IA [auth BI]	123	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JGR3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JGR3 Go to UniProtKB: Q5JGR3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JGR3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 35
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L10e	JA [auth BJ]	182	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JDI6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDI6 Go to UniProtKB: Q5JDI6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JDI6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 36
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L13	KA [auth BK]	142	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJF6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJF6 Go to UniProtKB: Q5JJF6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJF6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 37
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14	LA [auth BL]	141	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJF8 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJF8 Go to UniProtKB: Q5JJF8
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJF8
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 38
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L14e	MA [auth BM], NA [auth BN]	83	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJE4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJE4 Go to UniProtKB: Q5JJE4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJE4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 39
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15	OA [auth BO]	148	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJH0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJH0 Go to UniProtKB: Q5JJH0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJH0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 40
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L15e	PA [auth BP]	194	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JH43 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JH43 Go to UniProtKB: Q5JH43
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JH43
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 41
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18	QA [auth BQ]	201	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJG7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJG7 Go to UniProtKB: Q5JJG7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJG7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 42
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18e	RA [auth BR]	121	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJF5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJF5 Go to UniProtKB: Q5JJF5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJF5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 43
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L19e	SA [auth BS]	150	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJG6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJG6 Go to UniProtKB: Q5JJG6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJG6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 44
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L18Ae	TA [auth BT]	77	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JGT3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JGT3 Go to UniProtKB: Q5JGT3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JGT3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 45
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L21e	UA [auth BU]	98	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JI51 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JI51 Go to UniProtKB: Q5JI51
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JI51
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 46
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L22	VA [auth BV]	156	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JDH4 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDH4 Go to UniProtKB: Q5JDH4
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JDH4
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 47
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L23	WA [auth BW]	86	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JDH1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDH1 Go to UniProtKB: Q5JDH1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JDH1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 48
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24	XA [auth BX]	121	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJF9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJF9 Go to UniProtKB: Q5JJF9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJF9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 49
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L24e	YA [auth BY]	67	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JGR5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JGR5 Go to UniProtKB: Q5JGR5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JGR5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 50
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L29	ZA [auth BZ]	66	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JDH6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDH6 Go to UniProtKB: Q5JDH6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JDH6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 51
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30	AB [auth Ba]	155	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJG9 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJG9 Go to UniProtKB: Q5JJG9
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJG9
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 52
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L30e	BB [auth Bb]	102	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JE35 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JE35 Go to UniProtKB: Q5JE35
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JE35
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 53
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L31e	CB [auth Bc]	90	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JGT5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JGT5 Go to UniProtKB: Q5JGT5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JGT5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 54
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L32e	DB [auth Bd]	125	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJG5 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJG5 Go to UniProtKB: Q5JJG5
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJG5
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 55
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L34e	EB [auth Be]	90	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJF7 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJF7 Go to UniProtKB: Q5JJF7
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJF7
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 56
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L37Ae	FB [auth Bg]	86	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JDM6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JDM6 Go to UniProtKB: Q5JDM6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JDM6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 57
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L37e	GB [auth Bh]	63	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JIE1 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JIE1 Go to UniProtKB: Q5JIE1
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JIE1
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 58
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L39e	HB [auth Bi]	51	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JGT6 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JGT6 Go to UniProtKB: Q5JGT6
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JGT6
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 59
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L40e	IB [auth Bj]	51	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JJD3 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JJD3 Go to UniProtKB: Q5JJD3
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JJD3
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 60
Molecule	Chains	Sequence Length	Organism	Details	Image
LSU ribosomal protein L41E	JB [auth Bk]	37	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JEV0 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JEV0 Go to UniProtKB: Q5JEV0
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JEV0
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

| 3D Structure

Entity ID: 61
Molecule	Chains	Sequence Length	Organism	Details	Image
50S ribosomal protein L44e	KB [auth Bl]	94	Thermococcus kodakarensis KOD1	Mutation(s): 0
UniProt
Find proteins for Q5JE51 (Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)) Explore Q5JE51 Go to UniProtKB: Q5JE51
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q5JE51
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 1
16S ribosomal RNA	A [auth Aa]	1,498	Thermococcus kodakarensis KOD1
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 27
23S ribosomal RNA	AA [auth BA]	3,037	Thermococcus kodakarensis KOD1
Sequence Annotations Expand
Reference Sequence

Find similar nucleic acids by:

(by identity cutoff)

Molecule	Chains	Length	Organism
Entity ID: 28
5S ribosomal RNA	BA [auth BB]	126	Thermococcus kodakarensis KOD1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ZN Query on ZN Download:Ideal Coordinates CCD File SDF format, chain LB [auth Ag] SDF format, chain MB [auth Ar] SDF format, chain NB [auth As] SDF format, chain OB [auth Ax] SDF format, chain PB [auth Az] SDF format, chain QB [auth Az] SDF format, chain RB [auth BY] SDF format, chain SB [auth Be] SDF format, chain TB [auth Bg] SDF format, chain UB [auth Bh] SDF format, chain VB [auth Bj] SDF format, chain WB [auth Bl] MOL2 format, chain LB [auth Ag] MOL2 format, chain MB [auth Ar] MOL2 format, chain NB [auth As] MOL2 format, chain OB [auth Ax] MOL2 format, chain PB [auth Az] MOL2 format, chain QB [auth Az] MOL2 format, chain RB [auth BY] MOL2 format, chain SB [auth Be] MOL2 format, chain TB [auth Bg] MOL2 format, chain UB [auth Bh] MOL2 format, chain VB [auth Bj] MOL2 format, chain WB [auth Bl] mmCIF format, chain LB [auth Ag] mmCIF format, chain MB [auth Ar] mmCIF format, chain NB [auth As] mmCIF format, chain OB [auth Ax] mmCIF format, chain PB [auth Az] mmCIF format, chain QB [auth Az] mmCIF format, chain RB [auth BY] mmCIF format, chain SB [auth Be] mmCIF format, chain TB [auth Bg] mmCIF format, chain UB [auth Bh] mmCIF format, chain VB [auth Bj] mmCIF format, chain WB [auth Bl]	LB [auth Ag] MB [auth Ar] NB [auth As] OB [auth Ax] PB [auth Az] LB [auth Ag], MB [auth Ar], NB [auth As], OB [auth Ax], PB [auth Az], QB [auth Az], RB [auth BY], SB [auth Be], TB [auth Bg], UB [auth Bh], VB [auth Bj], WB [auth Bl]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain LB [auth Ag] Focus chain MB [auth Ar] Focus chain NB [auth As] Focus chain OB [auth Ax] Focus chain PB [auth Az] Focus chain QB [auth Az] Focus chain RB [auth BY] Focus chain SB [auth Be] Focus chain TB [auth Bg] Focus chain UB [auth Bh] Focus chain VB [auth Bj] Focus chain WB [auth Bl] Interactions & Density Focus chain LB [auth Ag] Focus chain MB [auth Ar] Focus chain NB [auth As] Focus chain OB [auth Ax] Focus chain PB [auth Az] Focus chain QB [auth Az] Focus chain RB [auth BY] Focus chain SB [auth Be] Focus chain TB [auth Bg] Focus chain UB [auth Bh] Focus chain VB [auth Bj] Focus chain WB [auth Bl]