1N34

Structure of the Thermus thermophilus 30S ribosomal subunit in the presence of codon and crystallographically disordered near-cognate transfer rna anticodon stem-loop mismatched at the first codon position


Macromolecule Annotations for the Entities in PDB 1N34

Domain Annotation: SCOP Classification SCOP Database (version: 1.75) Homepage

Chains Domain Info Class Fold Superfamily Family Domain Species
B d1n34b_ Alpha and beta proteins (a/b) Flavodoxin-like Ribosomal protein S2 Ribosomal protein S2 Ribosomal protein S2 Thermus thermophilus [TaxId: 274]
C2-106 d1n34c1 Alpha and beta proteins (a+b) Alpha-lytic protease prodomain-like Prokaryotic type KH domain (KH-domain type II) Prokaryotic type KH domain (KH-domain type II) Ribosomal protein S3 N-terminal domain Thermus thermophilus [TaxId: 274]
C107-207 d1n34c2 Alpha and beta proteins (a+b) Ribosomal protein S3 C-terminal domain Ribosomal protein S3 C-terminal domain Ribosomal protein S3 C-terminal domain Ribosomal protein S3 C-terminal domain Thermus thermophilus [TaxId: 274]
D d1n34d_ Alpha and beta proteins (a+b) Alpha-L RNA-binding motif Alpha-L RNA-binding motif Ribosomal protein S4 Ribosomal protein S4 Thermus thermophilus [TaxId: 274]
E74-154 d1n34e1 Alpha and beta proteins (a+b) Ribosomal protein S5 domain 2-like Ribosomal protein S5 domain 2-like Translational machinery components Ribosomal protein S5, C-terminal domain Thermus thermophilus [TaxId: 274]
E5-73 d1n34e2 Alpha and beta proteins (a+b) dsRBD-like dsRNA-binding domain-like Ribosomal S5 protein, N-terminal domain Ribosomal S5 protein, N-terminal domain Thermus thermophilus [TaxId: 274]
F d1n34f_ Alpha and beta proteins (a+b) Ferredoxin-like Ribosomal protein S6 Ribosomal protein S6 Ribosomal protein S6 Thermus thermophilus [TaxId: 274]
G d1n34g_ All alpha proteins Ribosomal protein S7 Ribosomal protein S7 Ribosomal protein S7 Ribosomal protein S7 Thermus thermophilus [TaxId: 274]
H d1n34h_ Alpha and beta proteins (a+b) Ribosomal protein S8 Ribosomal protein S8 Ribosomal protein S8 Ribosomal protein S8 Thermus thermophilus [TaxId: 274]
I d1n34i_ Alpha and beta proteins (a+b) Ribosomal protein S5 domain 2-like Ribosomal protein S5 domain 2-like Translational machinery components Ribosomal protein S9 Thermus thermophilus [TaxId: 274]
J d1n34j_ Alpha and beta proteins (a+b) Ferredoxin-like Ribosomal protein S10 Ribosomal protein S10 Ribosomal protein S10 Thermus thermophilus [TaxId: 274]
K d1n34k_ Alpha and beta proteins (a/b) Ribonuclease H-like motif Translational machinery components Ribosomal protein L18 and S11 Ribosomal protein S11 Thermus thermophilus [TaxId: 274]
L d1n34l_ All beta proteins OB-fold Nucleic acid-binding proteins Cold shock DNA-binding domain-like Ribosomal protein S12 Thermus thermophilus [TaxId: 274]
M d1n34m_ All alpha proteins S13-like H2TH domain S13-like H2TH domain Ribosomal protein S13 Ribosomal protein S13 Thermus thermophilus [TaxId: 274]
N d1n34n_ Small proteins Glucocorticoid receptor-like (DNA-binding domain) Glucocorticoid receptor-like (DNA-binding domain) Ribosomal protein S14 Ribosomal protein S14 Thermus thermophilus [TaxId: 274]
O d1n34o_ All alpha proteins S15/NS1 RNA-binding domain S15/NS1 RNA-binding domain Ribosomal protein S15 Ribosomal protein S15 Thermus thermophilus [TaxId: 274]
P d1n34p_ Alpha and beta proteins (a+b) Ribosomal protein S16 Ribosomal protein S16 Ribosomal protein S16 Ribosomal protein S16 Thermus thermophilus [TaxId: 274]
Q d1n34q_ All beta proteins OB-fold Nucleic acid-binding proteins Cold shock DNA-binding domain-like Ribosomal protein S17 Thermus thermophilus [TaxId: 274]
R d1n34r_ All alpha proteins DNA/RNA-binding 3-helical bundle Ribosomal protein S18 Ribosomal protein S18 Ribosomal protein S18 Thermus thermophilus [TaxId: 274]
S d1n34s_ Alpha and beta proteins (a+b) Ribosomal protein S19 Ribosomal protein S19 Ribosomal protein S19 Ribosomal protein S19 Thermus thermophilus [TaxId: 274]
T d1n34t_ All alpha proteins Spectrin repeat-like Ribosomal protein S20 Ribosomal protein S20 Ribosomal protein S20 Thermus thermophilus [TaxId: 274]
V d1n34v_ Peptides Arg-rich RNA binding peptides 30S ribosomal protein THX 30S ribosomal protein THX 30S ribosomal protein THX Thermus thermophilus [TaxId: 274]

Domain Annotation: CATH CATH Database (version 4.0.0) Homepage

Chains Domain Class Architecture Topology Homology
B2 1n34B02 Mainly Alpha Orthogonal Bundle Helix Hairpins Helix hairpin bin
C1 1n34C01 Alpha Beta 2-Layer Sandwich GMP Synthetase; Chain A, domain 3
C2 1n34C02 Alpha Beta 2-Layer Sandwich Ribosomal protein S3 C-terminal domain
D1 1n34D01 Mainly Alpha Orthogonal Bundle Ribosomal Protein S4 Delta 41; Chain A, domain 1 Ribosomal Protein S4 Delta 41; Chain A, domain 1
D2 1n34D02 Alpha Beta Roll Structural Genomics Hypothetical 15.5 Kd Protein In mrcA- pckA Intergenic Region; Chain A Structural Genomics Hypothetical 15.5 Kd Protein In Mrca- pcka Intergenic Region; Chain
E1 1n34E01 Alpha Beta 2-Layer Sandwich Double Stranded RNA Binding Domain
E2 1n34E02 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5; domain 2
F 1n34F00 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits
G 1n34G00 Mainly Alpha Orthogonal Bundle Ribosomal Protein S7 Ribosomal Protein S7;
H1 1n34H01 Alpha Beta 2-Layer Sandwich Ribosomal Protein S8; Chain: A, domain 1
H2 1n34H02 Alpha Beta 2-Layer Sandwich Dna Ligase; domain 1
I 1n34I00 Alpha Beta 2-Layer Sandwich Ribosomal Protein S5; domain 2
J 1n34J00 Alpha Beta 2-Layer Sandwich Alpha-Beta Plaits
K 1n34K00 Alpha Beta 2-Layer Sandwich Nucleotidyltransferase; domain 5
L 1n34L00 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
M1 1n34M01 Mainly Alpha Orthogonal Bundle Helicase, Ruva Protein; domain 3
M2 1n34M02 Few Secondary Structures Irregular 30s ribosomal protein s13; domain 2 30s ribosomal protein s13, domain 2
N 1n34N00 Few Secondary Structures Irregular 30s Ribosomal Protein S14; Chain N 30s Ribosomal Protein S14; Chain N
O 1n34O00 Mainly Alpha Orthogonal Bundle Helix Hairpins
P 1n34P00 Alpha Beta 2-Layer Sandwich S16 Ribosomal Protein; Chain: A;
Q 1n34Q00 Mainly Beta Beta Barrel OB fold (Dihydrolipoamide Acetyltransferase, E2P) Nucleic acid-binding proteins
R 1n34R00 Few Secondary Structures Irregular 30s Ribosomal Protein S18 30s Ribosomal Protein S18
S 1n34S00 Alpha Beta 2-Layer Sandwich 30s Ribosomal Protein S19; Chain A 30s Ribosomal Protein S19; Chain A
T 1n34T00 Mainly Alpha Up-down Bundle Methane Monooxygenase Hydroxylase; Chain G, domain 1

Protein Family Annotation Pfam Database Homepage

Chains Pfam Accession Pfam Identifier Pfam Description Type Source
N PF00253 Ribosomal_S14 Ribosomal protein S14p/S29e Family
D PF00163 Ribosomal_S4 Ribosomal protein S4/S9 N-terminal domain Family
L PF00164 Ribosom_S12_S23 Ribosomal protein S12/S23 Family
E PF00333 Ribosomal_S5 Ribosomal protein S5, N-terminal domain Domain PFAM PF00333
T PF01649 Ribosomal_S20p Ribosomal protein S20 Family
S PF00203 Ribosomal_S19 Ribosomal protein S19 Domain PFAM PF00203
K PF00411 Ribosomal_S11 Ribosomal protein S11 Family
R PF01084 Ribosomal_S18 Ribosomal protein S18 Family
F PF01250 Ribosomal_S6 Ribosomal protein S6 Domain PFAM PF01250
D PF01479 S4 S4 domain Domain The S4 domain is a small domain consisting of 60-65 amino acid residues that was detected in the bacterial ribosomal protein S4, eukaryotic ribosomal S9, two families of pseudouridine synthases, a novel family of predicted RNA methylases, a yeast protein containing a pseudouridine synthetase and a deaminase domain, bacterial tyrosyl-tRNA synthetases, and a number of uncharacterized, small proteins that may be involved in translation regulation [1]. The S4 domain probably mediates binding to RNA. PFAM PF01479
B PF00318 Ribosomal_S2 Ribosomal protein S2 Family
C PF07650 KH_2 KH domain Domain PFAM PF07650
C PF00189 Ribosomal_S3_C Ribosomal protein S3, C-terminal domain Domain This family contains a central domain Pfam:PF00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer. PFAM PF00189
H PF00410 Ribosomal_S8 Ribosomal protein S8 Domain PFAM PF00410
I PF00380 Ribosomal_S9 Ribosomal protein S9/S16 Family
M PF00416 Ribosomal_S13 Ribosomal protein S13/S18 Family
E PF03719 Ribosomal_S5_C Ribosomal protein S5, C-terminal domain Domain PFAM PF03719
J PF00338 Ribosomal_S10 Ribosomal protein S10p/S20e Family
G PF00177 Ribosomal_S7 Ribosomal protein S7p/S5e Domain This family contains ribosomal protein S7 from prokaryotes and S5 from eukaryotes. PFAM PF00177
Q PF00366 Ribosomal_S17 Ribosomal protein S17 Domain PFAM PF00366
O PF00312 Ribosomal_S15 Ribosomal protein S15 Domain PFAM PF00312
P PF00886 Ribosomal_S16 Ribosomal protein S16 Family

Gene Product Annotation Gene Ontology Consortium Homepage

Chains Polymer Molecular Function Biological Process Cellular Component
A 16S RIBOSOMAL RNA (1N34:A)
  • none
  • none
  • none
Z A-SITE MESSENGER RNA FRAGMENT (1N34:Z)
  • none
  • none
  • none
B 30S RIBOSOMAL PROTEIN S2 (1N34:B)
C 30S RIBOSOMAL PROTEIN S3 (1N34:C)
D 30S RIBOSOMAL PROTEIN S4 (1N34:D)
E 30S RIBOSOMAL PROTEIN S5 (1N34:E)
F 30S RIBOSOMAL PROTEIN S6 (1N34:F)
G 30S RIBOSOMAL PROTEIN S7 (1N34:G)
H 30S RIBOSOMAL PROTEIN S8 (1N34:H)
I 30S RIBOSOMAL PROTEIN S9 (1N34:I)
J 30S RIBOSOMAL PROTEIN S10 (1N34:J)
K 30S RIBOSOMAL PROTEIN S11 (1N34:K)
L 30S RIBOSOMAL PROTEIN S12 (1N34:L)
M 30S RIBOSOMAL PROTEIN S13 (1N34:M)
N 30S RIBOSOMAL PROTEIN S14 (1N34:N)
O 30S RIBOSOMAL PROTEIN S15 (1N34:O)
P 30S RIBOSOMAL PROTEIN S16 (1N34:P)
Q 30S RIBOSOMAL PROTEIN S17 (1N34:Q)
R 30S RIBOSOMAL PROTEIN S18 (1N34:R)
S 30S RIBOSOMAL PROTEIN S19 (1N34:S)
T 30S RIBOSOMAL PROTEIN S20 (1N34:T)
V 30S RIBOSOMAL PROTEIN THX (1N34:V)
  • none

Protein Modification Annotation

Type PDB Residue Nr. Description