6CFJ

Crystal structure of the Thermus thermophilus 70S ribosome in complex with histidyl-CAM and bound to mRNA and A-, P-, and E-site tRNAs at 2.8A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.8 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 

wwPDB Validation 3D Report Full Report


This is version 1.2 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 Chemistry and A.N. Belozersky Institute of Physico-Chemical Biology, Lomonosov Moscow State University, Moscow 119992, Russia.




Macromolecules

Find similar proteins by: Sequence  |  Structure


Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2
1D, 2D
276Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplB
Find proteins for Q72I07 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I07
Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3
1E, 2E
206Thermus thermophilusMutation(s): 0 
Gene Names: rplC (rpl3)
Find proteins for P52860 (Thermus thermophilus)
Go to UniProtKB:  P52860
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 thermophilusMutation(s): 0 
Gene Names: rplE (rpl5)
Find proteins for P41201 (Thermus thermophilus)
Go to UniProtKB:  P41201
Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L6
1H, 2H
180Thermus thermophilusMutation(s): 0 
Gene Names: rplF (rpl6)
Find proteins for P24316 (Thermus thermophilus)
Go to UniProtKB:  P24316
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 HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplM
Find proteins for Q72IN1 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IN1
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 thermophilusMutation(s): 0 
Gene Names: rplO (rpl15)
Find proteins for P74910 (Thermus thermophilus)
Go to UniProtKB:  P74910
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 HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplQ
Find proteins for Q72I33 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I33
Entity ID: 14
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L18
1S, 2S
112Thermus thermophilusMutation(s): 0 
Gene Names: rplR (rpl18)
Find proteins for P80320 (Thermus thermophilus)
Go to UniProtKB:  P80320
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 HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplT
Find proteins for Q72L76 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72L76
Entity ID: 17
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L21
1V, 2V
101Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplU
Find proteins for Q72HR2 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72HR2
Entity ID: 18
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L22
1W, 2W
113Thermus thermophilusMutation(s): 0 
Gene Names: rplV (rpl22)
Find proteins for P48286 (Thermus thermophilus)
Go to UniProtKB:  P48286
Entity ID: 19
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L23
1X, 2X
96Thermus thermophilusMutation(s): 0 
Gene Names: rplW
Find proteins for Q9RA57 (Thermus thermophilus)
Go to UniProtKB:  Q9RA57
Entity ID: 20
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L24
1Y, 2Y
110Thermus thermophilusMutation(s): 0 
Gene Names: rplX (rpl24)
Find proteins for Q56435 (Thermus thermophilus)
Go to UniProtKB:  Q56435
Entity ID: 21
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L25
1Z, 2Z
206Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rplY (ctc)
Find proteins for Q72IA7 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72IA7
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 HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmC
Find proteins for Q72I12 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72I12
Entity ID: 25
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L30
13, 23
60Thermus thermophilusMutation(s): 0 
Gene Names: rpmD (rpl30)
Find proteins for P74909 (Thermus thermophilus)
Go to UniProtKB:  P74909
Entity ID: 26
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L31
14, 24
71Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmE
Find proteins for Q72JR0 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72JR0
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 HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpmG
Find proteins for Q72GW3 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  Q72GW3
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 thermophilusMutation(s): 0 
Gene Names: rpmI (rpl35)
Find proteins for P80341 (Thermus thermophilus)
Go to UniProtKB:  P80341
Entity ID: 31
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L36
19, 29
37Thermus thermophilusMutation(s): 0 
Gene Names: rpmJ (rpl36)
Find proteins for P80256 (Thermus thermophilus)
Go to UniProtKB:  P80256
Entity ID: 33
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S2
1b, 2b
256Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsB (rps2)
Find proteins for P62662 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62662
Entity ID: 34
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S3
1c, 2c
239Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsC (rps3)
Find proteins for P62663 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62663
Entity ID: 35
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S4
1d, 2d
209Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsD (rps4)
Find proteins for P62664 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62664
Entity ID: 36
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S5
1e, 2e
162Thermus thermophilusMutation(s): 0 
Gene Names: rpsE (rps5)
Find proteins for P27152 (Thermus thermophilus)
Go to UniProtKB:  P27152
Entity ID: 37
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S6
1f, 2f
101Thermus thermophilusMutation(s): 0 
Gene Names: rpsF (rps6)
Find proteins for P23370 (Thermus thermophilus)
Go to UniProtKB:  P23370
Entity ID: 38
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S7
1g, 2g
156Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsG (rps7)
Find proteins for P62667 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62667
Entity ID: 39
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S8
1h, 2h
138Thermus thermophilusMutation(s): 0 
Gene Names: rpsH (rps8)
Find proteins for P24319 (Thermus thermophilus)
Go to UniProtKB:  P24319
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 thermophilusMutation(s): 0 
Gene Names: rpsJ (rps10)
Find proteins for P80375 (Thermus thermophilus)
Go to UniProtKB:  P80375
Entity ID: 42
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S11
1k, 2k
129Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsK (rps11)
Find proteins for P62654 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62654
Entity ID: 43
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S12
1l, 2l
132Thermus thermophilusMutation(s): 0 
Gene Names: rpsL (rps12)
Find proteins for P17293 (Thermus thermophilus)
Go to UniProtKB:  P17293
Entity ID: 44
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S13
1m, 2m
126Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsM (rps13)
Find proteins for P62655 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62655
Entity ID: 45
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S14 type Z
1n, 2n
61Thermus thermophilusMutation(s): 0 
Gene Names: rpsZ (rps14, rpsN)
Find proteins for P24320 (Thermus thermophilus)
Go to UniProtKB:  P24320
Entity ID: 46
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S15
1o, 2o
89Thermus thermophilusMutation(s): 0 
Gene Names: rpsO (rps15)
Find proteins for P80378 (Thermus thermophilus)
Go to UniProtKB:  P80378
Entity ID: 47
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S16
1p, 2p
88Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsP (rps16)
Find proteins for P62238 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62238
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 HB27 / ATCC BAA-163 / DSM 7039)Mutation(s): 0 
Gene Names: rpsR (rps18)
Find proteins for P62659 (Thermus thermophilus (strain HB27 / ATCC BAA-163 / DSM 7039))
Go to UniProtKB:  P62659
Entity ID: 50
MoleculeChainsSequence LengthOrganismDetails
30S ribosomal protein S19
1s, 2s
93Thermus thermophilusMutation(s): 0 
Gene Names: rpsS (rps19)
Find proteins for P80381 (Thermus thermophilus)
Go to UniProtKB:  P80381
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 thermophilusMutation(s): 0 
Gene Names: rpsU
Find proteins for P62612 (Thermus thermophilus)
Go to UniProtKB:  P62612
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
Entity ID: 53
MoleculeChainsLengthOrganism
mRNA1v,2v24Escherichia virus T4
Entity ID: 54
MoleculeChainsLengthOrganism
A-site and E-site tRNAs1w,1y,2w,2y76Escherichia coli
Entity ID: 55
MoleculeChainsLengthOrganism
P-site tRNA1x,2x77Salmonella enterica subsp. enterica serovar Gallinarum str. 287/91
Small Molecules
Ligands 5 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
Download SDF File 
Download CCD File 
1d, 2d
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC
 Ligand Interaction
ZN
Query on ZN
Download SDF File 
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, 12, 13, 15, 16, 17, 18, 19, 1a, 1A, 1B, 1b, 1D, 1e, 1E, 1f, 1F, 1G, 1I, 1l, 1m, 1n, 1N, 1O, 1p, 1P, 1q, 1Q, 1r, 1R, 1s, 1S, 1t, 1T, 1U, 1V, 1v, 1W, 1w, 1X, 1x, 1Y, 1y, 1Z, 20, 21, 23, 25, 27, 28, 2a, 2A, 2B, 2d, 2D, 2e, 2E, 2f, 2F, 2g, 2G, 2j, 2l, 2O, 2P, 2Q, 2q, 2R, 2r, 2t, 2T, 2U, 2V, 2v, 2w, 2W, 2X, 2x, 2y, 2Z
MAGNESIUM ION
Mg
JLVVSXFLKOJNIY-UHFFFAOYSA-N
 Ligand Interaction
EZG
Query on EZG
Download SDF File 
Download CCD File 
1A, 2A
N-[(1R,2R)-1,3-dihydroxy-1-(4-nitrophenyl)propan-2-yl]-L-histidinamide
C15 H19 N5 O5
MMDMFLDVXHCRMV-BFHYXJOUSA-N
 Ligand Interaction
Modified Residues  15 Unique
IDChainsTypeFormula2D DiagramParent
PSU
Query on PSU
1a, 1A, 1w, 1x, 1y, 2a, 2A, 2w, 2x, 2y
RNA LINKINGC9 H13 N2 O9 PU
5MC
Query on 5MC
1a, 1A, 1x, 2a, 2A, 2x
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
4SU
Query on 4SU
1w, 1x, 1y, 2w, 2x, 2y
RNA LINKINGC9 H13 N2 O8 P SU
MIA
Query on MIA
1w, 1y, 2w, 2y
RNA LINKINGC16 H26 N5 O7 P SA
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, 1w, 1y, 2a, 2w, 2y
RNA LINKINGC11 H18 N5 O8 PG
5MU
Query on 5MU
1A, 1w, 1x, 1y, 2A, 2w, 2x, 2y
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: 2.8 Å
  • R-Value Free: 0.269 
  • R-Value Work: 0.214 
  • Space Group: P 21 21 21
Unit Cell:
Length (Å)Angle (°)
a = 209.780α = 90.00
b = 449.830β = 90.00
c = 622.740γ = 90.00
Software Package:
Software NamePurpose
XDSdata reduction
Cootmodel building
PDB_EXTRACTdata extraction
XSCALEdata scaling
PHASERphasing
PHENIXrefinement

Structure Validation

View Full Validation Report or Ramachandran Plots


View more in-depth experimental data

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 DiseasesUnited 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: 2019-02-20
    Type: Author supporting evidence, Data collection