6XHY

Crystal structure of the Thermus thermophilus 70S ribosome in complex with telithromycin, mRNA, aminoacylated A- and P-site tRNAs, and deacylated E-site tRNA at 2.60A resolution

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.60 Å
  • R-Value Free: 0.266 
  • R-Value Work: 0.217 
  • R-Value Observed: 0.219 

wwPDB Validation   3D Report Full Report


This is version 1.1 of the entry. See complete history. 


Literature

Structure of Erm-modified 70S ribosome reveals the mechanism of macrolide resistance.

Svetlov, M.S., Syroegin, E.A., Aleksandrova, E.V., Atkinson, G.C., Gregory, S.T., Mankin, A.S., Polikanov, Y.S.

(2021) Nat Chem Biol 


Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L21D, 2D276Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplB, TTHA1689
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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L31E, 2E206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplC, TTHA1692
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L41F, 2F210Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplD, TTHA1691
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L51G, 2G182Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplE, TTHA1680
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L61H, 2H180Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplF, TTHA1677
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L91I, 2I148Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplI, TTHA0242
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Entity ID: 9
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50S ribosomal protein L131N, 2N140Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplM, TTHA1465
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Entity ID: 10
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L141O, 2O122Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplN, TTHA1682
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Entity ID: 11
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L151P, 2P150Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplO, TTHA1673
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Entity ID: 12
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50S ribosomal protein L161Q, 2Q141Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplP, TTHA1685
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Entity ID: 13
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50S ribosomal protein L171R, 2R118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplQ, rpl17, TTHA1663
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Entity ID: 14
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L181S, 2S112Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplR, TTHA1676
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Entity ID: 15
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50S ribosomal protein L191T, 2T146Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplS, TTHA1031
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Entity ID: 16
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L201U, 2U118Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplT, TTHA0553
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Entity ID: 17
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L211V, 2V101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplU, TTHA1783
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Entity ID: 18
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L221W, 2W113Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplV, TTHA1687
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Entity ID: 19
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50S ribosomal protein L231X, 2X96Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplW, TTHA1690
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Entity ID: 20
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50S ribosomal protein L241Y, 2Y110Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplX, TTHA1681
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Entity ID: 21
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50S ribosomal protein L251Z, 2Z206Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rplY, rpl25, rptL5, TTHA1589
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Entity ID: 22
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50S ribosomal protein L2710, 2085Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmA, TTHA1782
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Entity ID: 23
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50S ribosomal protein L2811, 2198Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmB, TTHA0042
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Entity ID: 24
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50S ribosomal protein L2912, 2272Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmC, TTHA1684
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Entity ID: 25
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3013, 2360Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmD, TTHA1674
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Entity ID: 26
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3114, 2471Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmE, TTHA1073
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Entity ID: 27
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3215, 2560Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmF, rpl32, TTHA0418
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Entity ID: 28
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50S ribosomal protein L3316, 2654Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmG, rpl33, TTHA0250
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Entity ID: 29
MoleculeChainsSequence LengthOrganismDetailsImage
50S ribosomal protein L3417, 2749Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmH, rpl34, TTHA0446
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Entity ID: 30
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50S ribosomal protein L3518, 2865Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmI, TTHA0552
Find proteins for Q5SKU1 (Thermus thermophilus (strain HB8 / ATCC 27634 / DSM 579))
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Entity ID: 31
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50S ribosomal protein L3619, 2937Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpmJ, TTHA1668
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Entity ID: 33
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S21b, 2b256Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsB, rps2, TTHA0861
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Entity ID: 34
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S31c, 2c239Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsC, rps3, TTHA1686
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Entity ID: 35
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S41d, 2d209Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsD, rps4, TTHA1665
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Entity ID: 36
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S51e, 2e162Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsE, TTHA1675
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Entity ID: 37
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30S ribosomal protein S61f, 2f101Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsF, TTHA0245
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Entity ID: 38
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30S ribosomal protein S71g, 2g156Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsG, rps7, TTHA1696
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Entity ID: 39
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S81h, 2h138Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsH, TTHA1678
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Entity ID: 40
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30S ribosomal protein S91i, 2i128Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsI, rps9, TTHA1464
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Entity ID: 41
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30S ribosomal protein S101j, 2j105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsJ, TTHA1693
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Entity ID: 42
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30S ribosomal protein S111k, 2k129Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsK, rps11, TTHA1666
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Entity ID: 43
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30S ribosomal protein S121l, 2l132Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsL, TTHA1697
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Entity ID: 44
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30S ribosomal protein S131m, 2m126Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsM, rps13, TTHA1667
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Entity ID: 45
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30S ribosomal protein S14 type Z1n, 2n61Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsZ, rpsN, TTHA1679
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Entity ID: 46
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30S ribosomal protein S151o, 2o89Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsO, TTHA1138
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Entity ID: 47
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30S ribosomal protein S161p, 2p88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsP, TTHA1035
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Entity ID: 48
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S171q, 2q105Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsQ, TTHA1683
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Entity ID: 49
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S181r, 2r88Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsR, TTHA0243
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Entity ID: 50
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein S191s, 2s93Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsS, TTHA1688
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Entity ID: 51
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30S ribosomal protein S201t, 2t106Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsT, rps20, TTHA1397
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Entity ID: 52
MoleculeChainsSequence LengthOrganismDetailsImage
30S ribosomal protein Thx1u, 2u27Thermus thermophilus HB8Mutation(s): 0 
Gene Names: rpsU, TTHA1396
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Entity ID: 1
MoleculeChainsLengthOrganismImage
23S Ribosomal RNA1A, 2A2915Thermus thermophilus HB8
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Entity ID: 2
MoleculeChainsLengthOrganismImage
5S Ribosomal RNA1B, 2B121Thermus thermophilus HB8
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Entity ID: 32
MoleculeChainsLengthOrganismImage
16S Ribosomal RNA1a, 2a1521Thermus thermophilus HB8
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Entity ID: 53
MoleculeChainsLengthOrganismImage
mRNA1v, 2v24Escherichia virus T4
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Entity ID: 54
MoleculeChainsLengthOrganismImage
A-site tRNA1w, 2w76Escherichia coli
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Entity ID: 55
MoleculeChainsLengthOrganismImage
P-site tRNA1x, 2x77Escherichia coli
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Entity ID: 56
MoleculeChainsLengthOrganismImage
E-site tRNA1y, 2y76Escherichia coli
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
TEL
Query on TEL
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1A, 2A
TELITHROMYCIN
C43 H65 N5 O10
LJVAJPDWBABPEJ-PNUFFHFMSA-N		 Ligand Interaction
SF4
Query on SF4
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1d, 2d
IRON/SULFUR CLUSTER
Fe4 S4
LJBDFODJNLIPKO-VKOJMFJBAC		 Ligand Interaction
ZN
Query on ZN
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14, 15, 16, 19, 1Y, 1n, 24, 25, 26, 29, 2Y, 2n
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N		 Ligand Interaction
K
Query on K
Download Ideal Coordinates CCD File 
1A, 2x
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N		 Ligand Interaction
MG
Query on MG
Download Ideal Coordinates CCD File