6WYV

E. coli 50S ribosome bound to compounds 47 and VS1


Experimental Data Snapshot

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

wwPDB Validation 3D Report Full Report



Literature

Synthesis and mechanism of action of group A streptogramin antibiotics that overcome resistance

Pellegrino, J.Li, Q.Lee, D.J.Tran, A.A.Wang, R.Chaires, H.A.Park, J.E.Ji, K.Chow, D.Zhang, N.Brilot, A.F.Biel, J.T.van Zundert, G.Borrelli, K.Shinabarger, D.Wolfe, C.Murray, B.Jacobson, M.P.Seiple, I.B.Fraser, J.S.

To be published.

Macromolecules

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Entity ID: 3
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L2K271Escherichia coliMutation(s): 0 
Find proteins for P60422 (Escherichia coli (strain K12))
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Go to UniProtKB:  P60422
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  • Reference Sequence

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Entity ID: 4
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L15L144Escherichia coliMutation(s): 0 
Gene Names: 
rplOA8C65_19395A9R57_24660ACU57_21045AM464_09135AUQ13_22145BANRA_01932BANRA_03684BHS87_18545BJJ90_02210BMA87_18510BON75_18850BUE81_25610BvCms2454_01416BvCmsHHP001_00334BvCmsHHP019_04131BvCmsHHP056_02703BvCmsKSP026_02554BvCmsSINP011_02480BW690_10710BZL31_22885C5N07_23575C9E25_20065C9Z39_20710CA593_09735CG692_20270CI693_13520CI694_01990CIG45_22410D0X26_24495D2185_22985D3821_17755D3O91_20305D3Y67_24390D4638_19455D4718_17880D9C99_17930D9D20_21995D9D44_22490D9G29_15635D9G69_20945D9H68_17710D9J52_19090D9Z28_15390DAH37_14685DBQ99_03415DJ503_19770DL326_22310DNC98_19095DT034_22410DTL43_21000E2119_19640E2134_21880E2135_06185E4K55_21420E4K60_18985E4K61_20025E5P22_10480E5P28_20875EA213_19860EAI42_04990EAI52_16365EC1094V2_354EC3234A_55c00230EC3426_04459ECTO6_00449ED307_17010EEP23_17135EG808_17075EI021_21030EI028_20740EI032_18995EI041_20035EIZ86_16985EIZ93_12470EL75_0396EL79_0415EL80_0407ELT20_19170EPT01_19765ERS085365_03907ERS085416_03881ERS139211_03685ERS150873_04051EXX71_21335EYD11_02080F1E19_19655FRV13_20015FV293_22465FWK02_06270GHR40_07050GKF74_18130GKF86_20070GKF89_18470GP689_20785GQE34_14255GQE64_20420GQM17_19915GRW42_19350GRW80_20585NCTC10963_00456NCTC11022_03475NCTC11126_02772NCTC12650_00710NCTC13216_01351NCTC9045_00567NCTC9062_02686NCTC9117_00757NCTC9706_02738PGD_00585RK56_021420SAMEA3472047_03862SAMEA3472080_04748SAMEA3484427_04887SAMEA3484429_04875SAMEA3752559_00346SAMEA3753300_02227

Find proteins for A0A037Y8L6 (Escherichia coli)
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Go to UniProtKB:  A0A037Y8L6
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Entity ID: 5
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L4M201Escherichia coliMutation(s): 0 
Find proteins for D7Z9F6 (Escherichia coli MS 69-1)
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Entity ID: 6
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L3N209Escherichia coliMutation(s): 0 
Find proteins for P60438 (Escherichia coli (strain K12))
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Go to UniProtKB:  P60438
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Entity ID: 7
MoleculeChainsSequence LengthOrganismDetails
50S ribosomal protein L13O142Escherichia coliMutation(s): 0 
Find proteins for D7ZET0 (Escherichia coli MS 69-1)
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Entity ID: 8
MoleculeChainsSequence LengthOrganismDetails
VIRGINIAMYCIN S1C7Streptomyces virginiaeMutation(s): 0 
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Entity ID: 1
MoleculeChainsLengthOrganism
23S ribosomal RNAI2904Escherichia coli

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Entity ID: 2
MoleculeChainsLengthOrganism
5S ribosomal RNAJ118Escherichia coli
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
O7S
Query on O7S

Download CCD File 
I
(3R,4R,5E,10E,12E,14S,16R,26aR)-16-fluoro-14-hydroxy-12-methyl-3-(propan-2-yl)-4-(prop-2-en-1-yl)-3,4,8,9,14,15,16,17,24,25,26,26a-dodecahydro-1H,7H,22H-21,18-(azeno)pyrrolo[2,1-c][1,8,4,19]dioxadiazacyclotetracosine-1,7,22-trione
C30 H40 F N3 O6
GWIAEMBAGQHJHW-CLECSTCYSA-N
 Ligand Interaction
Biologically Interesting Molecules 1 Unique
IDChainsNameType/Class2D Diagram3D Interactions
PRD_000227
Query on PRD_000227
CVIRGINIAMYCIN S1C /  Antibiotic, Antimicrobial

--

Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
MEA
Query on MEA
CL-PEPTIDE LINKINGC10 H13 N O2PHE
Experimental Data & Validation

Experimental Data

  • Method: ELECTRON MICROSCOPY
  • Resolution: 2.75 Å
  • Aggregation State: PARTICLE 
  • Reconstruction Method: SINGLE PARTICLE 

Structure Validation

View Full Validation Report



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM123159
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)United StatesGM124149

Revision History 

  • Version 1.0: 2020-06-17
    Type: Initial release