6CFL

Crystal structure of the Thermus thermophilus 70S ribosome in complex with lysyl-CAM and bound to protein Y (YfiA) at 2.6A resolution


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.209 

wwPDB Validation 3D Report Full Report


This is version 1.4 of the entry. See complete history

Literature

Binding and Action of Amino Acid Analogs of Chloramphenicol upon the Bacterial Ribosome.

Tereshchenkov, A.G.Dobosz-Bartoszek, M.Osterman, I.A.Marks, J.Sergeeva, V.A.Kasatsky, P.Komarova, E.S.Stavrianidi, A.N.Rodin, I.A.Konevega, A.L.Sergiev, P.V.Sumbatyan, N.V.Mankin, A.S.Bogdanov, A.A.Polikanov, Y.S.

(2018) J. Mol. Biol. 430: 842-852

  • DOI: 10.1016/j.jmb.2018.01.016
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 
  • Antibiotic chloramphenicol (CHL) binds with a moderate affinity at the peptidyl transferase center of the bacterial ribosome and inhibits peptide bond formation. As an approach for modifying and potentially improving properties of this inhibitor, we ...

    Antibiotic chloramphenicol (CHL) binds with a moderate affinity at the peptidyl transferase center of the bacterial ribosome and inhibits peptide bond formation. As an approach for modifying and potentially improving properties of this inhibitor, we explored ribosome binding and inhibitory activity of a number of amino acid analogs of CHL. The L-histidyl analog binds to the ribosome with the affinity exceeding that of CHL by 10 fold. Several of the newly synthesized analogs were able to inhibit protein synthesis and exhibited the mode of action that was distinct from the action of CHL. However, the inhibitory properties of the semi-synthetic CHL analogs did not correlate with their affinity and in general, the amino acid analogs of CHL were less active inhibitors of translation in comparison with the original antibiotic. The X-ray crystal structures of the Thermus thermophilus 70S ribosome in complex with three semi-synthetic analogs showed that CHL derivatives bind at the peptidyl transferase center, where the aminoacyl moiety of the tested compounds established idiosyncratic interactions with rRNA. Although still fairly inefficient inhibitors of translation, the synthesized compounds represent promising chemical scaffolds that target the peptidyl transferase center of the ribosome and potentially are suitable for further exploration.


    Organizational Affiliation

    Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA. Electronic address: yuryp@uic.edu.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia; Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia.,Petersburg Nuclear Physics Institute, NRC "Kurchatov Institute", Gatchina 188300, Russia; Peter the Great St. Petersburg Polytechnic University, Saint Petersburg 195251, Russia.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.,Center for Biomolecular Sciences, University of Illinois, Chicago, IL 60607, USA; Department of Medicinal Chemistry and Pharmacognosy, University of Illinois at Chicago, Chicago, IL 60607, USA.,Petersburg Nuclear Physics Institute, NRC "Kurchatov Institute", Gatchina 188300, Russia.,Department of Biological Sciences, University of Illinois at Chicago, Chicago, IL 60607, USA.,Skolkovo Institute of Science and Technology, Skolkovo, Moscow region 143025, Russia; Department of Bioengineering and Bioinformatics, Lomonosov Moscow State University, Moscow 119992, Russia.,Department of Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia. Electronic address: bogdanov@belozersky.msu.ru.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
1D, 2D
276Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplB
Find proteins for P60405 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60405
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L3
1E, 2E
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplC
Find proteins for Q5SHN8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN8
Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4
1F, 2F
210Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplD
Find proteins for Q5SHN9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN9
Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L5
1G, 2G
182Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplE
Find proteins for Q5SHQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ0
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
1H, 2H
180Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplF
Find proteins for P0DOY8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY8
Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L9
1I, 2I
148Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplI
Find proteins for Q5SLQ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ1
Entity ID: 9
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13
1N, 2N
140Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplM
Find proteins for P60488 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60488
Entity ID: 10
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L14
1O, 2O
122Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplN
Find proteins for Q5SHP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP8
Entity ID: 11
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15
1P, 2P
150Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplO
Find proteins for Q5SHQ7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ7
Entity ID: 12
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L16
1Q, 2Q
141Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplP
Find proteins for P60489 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60489
Entity ID: 13
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L17
1R, 2R
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplQ (rpl17)
Find proteins for Q9Z9H5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q9Z9H5
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L18
1S, 2S
112Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplR
Find proteins for Q5SHQ4 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ4
Entity ID: 15
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L19
1T, 2T
146Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplS
Find proteins for P60490 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60490
Entity ID: 16
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L20
1U, 2U
118Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplT
Find proteins for P60491 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60491
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
1V, 2V
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplU
Find proteins for P60492 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60492
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
1W, 2W
113Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplV
Find proteins for Q5SHP3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP3
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
1X, 2X
96Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplW
Find proteins for Q5SHP0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP0
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L24
1Y, 2Y
110Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplX
Find proteins for Q5SHP9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP9
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
1Z, 2Z
206Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rplY (rpl25, rptL5)
Find proteins for Q5SHZ1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHZ1
Entity ID: 22
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L27
10, 20
85Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmA
Find proteins for P60493 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60493
Entity ID: 23
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L28
11, 21
98Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmB
Find proteins for P60494 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P60494
Entity ID: 24
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L29
12, 22
72Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q5SHP6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP6
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
13, 23
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmD
Find proteins for Q5SHQ6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ6
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S Ribosomal Protein L31
14, 24
71Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmE
Find proteins for Q5SJE1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJE1
Entity ID: 27
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L32
15, 25
60Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmF (rpl32)
Find proteins for P80339 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80339
Entity ID: 28
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L33
16, 26
54Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmG (rpl33)
Find proteins for P35871 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P35871
Entity ID: 29
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L34
17, 27
49Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmH (rpl34)
Find proteins for P80340 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80340
Entity ID: 30
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L35
18, 28
65Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmI
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SKU1
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
19, 29
37Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpmJ
Find proteins for Q5SHR2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHR2
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
1b, 2b
256Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P80371 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80371
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
1c, 2c
239Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P80372 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80372
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
1d, 2d
209Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P80373 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80373
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
1e, 2e
162Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsE
Find proteins for Q5SHQ5 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHQ5
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
1f, 2f
101Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsF
Find proteins for Q5SLP8 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLP8
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
1g, 2g
156Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P17291 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P17291
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein S8
1h, 2h
138Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsH
Find proteins for P0DOY9 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY9
Entity ID: 40
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S9
1i, 2i
128Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsI (rps9)
Find proteins for P80374 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80374
Entity ID: 41
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S10
1j, 2j
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsJ
Find proteins for Q5SHN7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN7
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
1k, 2k
129Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P80376 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80376
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
1l, 2l
132Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsL
Find proteins for Q5SHN3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHN3
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
1m, 2m
126Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P80377 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80377
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
1n, 2n
61Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsZ (rpsN)
Find proteins for P0DOY6 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY6
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
1o, 2o
89Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsO
Find proteins for Q5SJ76 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJ76
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
1p, 2p
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsP
Find proteins for Q5SJH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SJH3
Entity ID: 48
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S17
1q, 2q
105Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsQ
Find proteins for P0DOY7 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P0DOY7
Entity ID: 49
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S18
1r, 2r
88Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsR
Find proteins for Q5SLQ0 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SLQ0
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
1s, 2s
93Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsS
Find proteins for Q5SHP2 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SHP2
Entity ID: 51
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S20
1t, 2t
106Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsT (rps20)
Find proteins for P80380 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  P80380
Entity ID: 52
MoleculeChainsSequence LengthOrganismDetails
30S Ribosomal Protein THX
1u, 2u
27Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579)Mutation(s): 0 
Gene Names: rpsU
Find proteins for Q5SIH3 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
Go to UniProtKB:  Q5SIH3
Entity ID: 53
MoleculeChainsSequence LengthOrganismDetails
Protein Y
1y, 2y
113Escherichia coli O157:H7Mutation(s): 0 
Gene Names: yfiA (raiA)
Find proteins for P0AD51 (Escherichia coli O157:H7)
Go to UniProtKB:  P0AD51
Entity ID: 1
MoleculeChainsLengthOrganism
23S Ribosomal RNA1A,2A2915Thermus thermophilus HB8
Entity ID: 2
MoleculeChainsLengthOrganism
5S Ribosomal RNA1B,2B121Thermus thermophilus HB8
Entity ID: 32
MoleculeChainsLengthOrganism
16S Ribosomal RNA1a,2a1521Thermus thermophilus HB8
Small Molecules
Ligands 7 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
1A, 2A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
SF4
Query on SF4

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Download CCD File 
1d, 2d
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
EZM
Query on EZM

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Download CCD File 
1A, 2A
N-[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]-L-lysinamide
C15 H24 N4 O5
LSXOPXJWOLKWDK-BFHYXJOUSA-N
 Ligand Interaction
ZN
Query on ZN

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Download CCD File 
14, 15, 16, 19, 1n, 1Y, 24, 25, 26, 29, 2n, 2Y
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
MG
Query on MG

Download SDF File 
Download CCD File 
10, 11, 13, 14, 15, 17, 18, 19, 1a, 1A, 1b, 1B, 1d, 1D, 1E, 1e, 1f, 1F, 1G, 1g, 1h, 1H, 1i, 1k, 1l, 1n, 1N, 1O, 1o, 1P, 1p, 1q, 1Q, 1R, 1t, 1T, 1U, 1V, 1W, 1X, 1y, 1Z, 20, 21, 23, 25, 28, 2a, 2A, 2B, 2d, 2D, 2e, 2E, 2F, 2f, 2G, 2I, 2j, 2N, 2O, 2P, 2Q, 2R, 2t, 2T, 2V, 2W, 2X
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
ARG
Query on ARG

Download SDF File 
Download CCD File 
1B, 1F
ARGININE
C6 H15 N4 O2
ODKSFYDXXFIFQN-BYPYZUCNSA-O
 Ligand Interaction
MPD
Query on MPD

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Download CCD File 
18, 1a, 1A, 1T, 2A, 2B
(4S)-2-METHYL-2,4-PENTANEDIOL
C6 H14 O2
SVTBMSDMJJWYQN-YFKPBYRVSA-N
 Ligand Interaction
Modified Residues  13 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
1a, 1A, 2A, 2a
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
1A, 1a, 2a, 2A
RNA LINKINGC10 H16 N3 O8 PC
M2G
Query on M2G
1a, 2a
RNA LINKINGC12 H18 N5 O8 PG
MA6
Query on MA6
1a, 2a
RNA LINKINGC12 H18 N5 O7 PA
2MG
Query on 2MG
1a, 2a
RNA LINKINGC11 H16 N5 O8 PG
UR3
Query on UR3
1a, 2a
RNA LINKINGC10 H15 N2 O9 PU
OMG
Query on OMG
1A, 2A
RNA LINKINGC11 H16 N5 O8 PG
7MG
Query on 7MG
1a, 2a
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
1A, 2A
RNA LINKINGC10 H15 N2 O9 PU
2MA
Query on 2MA
1A, 2A
RNA LINKINGC11 H16 N5 O7 PA
2MU
Query on 2MU
1A, 2A
RNA LINKINGC11 H17 N2 O9 PU
0TD
Query on 0TD
1l, 2l
L-PEPTIDE LINKINGC5 H9 N O4 SASP
4OC
Query on 4OC
1a, 1A, 2a, 2A
RNA LINKINGC11 H18 N3 O8 PC
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.6 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.209 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 210.150α = 90.00
b = 449.330β = 90.00
c = 623.460γ = 90.00
Software Package:
Software NamePurpose
Cootmodel building
PHASERphasing
XSCALEdata scaling
PHENIXrefinement
XDSdata reduction
PDB_EXTRACTdata extraction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
Illinois State Startup FundsUnited States--
Russian Science FoundationRussian Federation14-24-00061-P
Russian Foundation for Basic ResearchRussian Federation16-04-00709
Russian Foundation for Basic ResearchRussian Federation15-34-20139
National Institutes of Health/National Institute Of Allergy and Infectious Diseases (NIH/NIAID)United StatesRO1 AI125518

Revision History 

  • Version 1.0: 2018-03-07
    Type: Initial release
  • Version 1.1: 2018-03-28
    Type: Data collection, Database references
  • Version 1.2: 2018-04-11
    Type: Data collection, Database references
  • Version 1.3: 2019-02-20
    Type: Author supporting evidence, Data collection
  • Version 1.4: 2019-12-18
    Type: Author supporting evidence