Structure of PDB 3vmt Chain A Binding Site BS01

Receptor Information
>3vmt Chain A (length=222) Species: 158878 (Staphylococcus aureus subsp. aureus Mu50) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
RILLKILLTILIIIALFIGIMYFLSTRDNVDELRKIENKSSFVSADNMPE
YVKGAFISMEDERFYNHHGFDLKGTTRALFSTGGSTITQQVVKNYFYDND
RSFTRKVKELFVAHRVEKQYNKNEILSFYLNNIYFGDNQYTLEGAANHYF
GTTVNKNSTTMSHITVLQSAILASKVNAPSVYNINNMSENFTQRVSTNLE
KMKQQNYINETQYQQAMSQLNR
Ligand information
Ligand IDLHI
InChIInChI=1S/C93H155N7O23P2S/c1-62(2)29-19-30-63(3)31-20-32-64(4)33-21-34-65(5)35-22-36-66(6)37-23-38-67(7)39-24-40-68(8)41-25-42-69(9)43-26-44-70(10)45-27-46-71(11)47-28-48-72(12)51-54-117-124(111,112)123-125(113,114)122-92-84(98-76(16)104)88(87(79(60-102)120-92)121-91-83(97-75(15)103)86(107)85(106)78(59-101)119-91)118-74(14)90(109)96-73(13)89(108)95-53-56-116-58-57-115-55-52-94-81(105)50-18-17-49-80-82-77(61-126-80)99-93(110)100-82/h29,31,33,35,37,39,41,43,45,47,51,73-74,77-80,82-88,91-92,101-102,106-107H,17-28,30,32,34,36,38,40,42,44,46,48-50,52-61H2,1-16H3,(H,94,105)(H,95,108)(H,96,109)(H,97,103)(H,98,104)(H,111,112)(H,113,114)(H2,99,100,110)/b63-31-,64-33?,65-35?,66-37?,67-39-,68-41-,69-43-,70-45?,71-47?,72-51-/t73-,74+,77-,78+,79+,80-,82-,83+,84+,85-,86+,87+,88+,91-,92+/m0/s1
InChIKeyWLFSVWBINOGDFX-PARYEQGPSA-N
SMILES
SoftwareSMILES
CC(C(=O)NCCOCCOCCNC(=O)CCCCC1C2C(CS1)NC(=O)N2)NC(=O)C(C)OC3C(C(OC(C3OC4C(C(C(C(O4)CO)O)O)NC(=O)C)CO)OP(=O)(O)OP(=O)(O)OCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C)NC(=O)C
C[C@H](NC(=O)[C@@H](C)O[C@@H]1[C@@H](NC(C)=O)[C@H](O[C@H](CO)[C@H]1O[C@@H]2O[C@H](CO)[C@H](O)[C@H](O)[C@H]2NC(C)=O)O[P](O)(=O)O[P](O)(=O)OC\C=C(C)/CC/C=C(C)/CC/C=C(C)/CC\C=C(C)/CC\C=C(C)/CC\C=C(C)/CC/C=C(C)/CC/C=C(C)/CC/C=C(C)/CC\C=C(C)/CCC=C(C)C)C(=O)NCCOCCOCCNC(=O)CCCC[C@@H]3SC[C@@H]4NC(=O)N[C@H]34
C[CH](NC(=O)[CH](C)O[CH]1[CH](NC(C)=O)[CH](O[CH](CO)[CH]1O[CH]2O[CH](CO)[CH](O)[CH](O)[CH]2NC(C)=O)O[P](O)(=O)O[P](O)(=O)OCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C)C(=O)NCCOCCOCCNC(=O)CCCC[CH]3SC[CH]4NC(=O)N[CH]34
C[C@@H](C(=O)NCCOCCOCCNC(=O)CCCC[C@H]1[C@@H]2[C@H](CS1)NC(=O)N2)NC(=O)[C@@H](C)O[C@@H]3[C@H]([C@H](O[C@@H]([C@H]3O[C@H]4[C@@H]([C@H]([C@H]([C@H](O4)CO)O)O)NC(=O)C)CO)OP(=O)(O)OP(=O)(O)OCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)CCC=C(C)C)NC(=O)C
FormulaC93 H155 N7 O23 P2 S
Name[(2R,3R,4R,5S,6R)-4-[(2R)-1-[[(2S)-1-[2-[2-[2-[5-[(3aS,4S,6aR)-2-oxidanylidene-1,3,3a,4,6,6a-hexahydrothieno[3,4-d]imidazol-4-yl]pentanoylamino]ethoxy]ethoxy]ethylamino]-1-oxidanylidene-propan-2-yl]amino]-1-oxidanylidene-propan-2-yl]oxy-3-acetamido-5-[(2S,3R,4R,5R,6R)-3-acetamido-6-(hydroxymethyl)-4,5-bis(oxidanyl)oxan-2-yl]oxy-6-(hydroxymethyl)oxan-2-yl] [oxidanyl(3,7,11,15,19,23,27,31,35,39,43-undecamethyltetratetraconta-2,6,10,14,18,22,26,30,34,38,42-undecaenoxy)phosphoryl] hydrogen phosphate
ChEMBL
DrugBank
ZINC
PDB chain3vmt Chain A Residue 301 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3vmt Crystal structure of Staphylococcus aureus transglycosylase in complex with a lipid II analog and elucidation of peptidoglycan synthesis mechanism
Resolution2.299 Å
Binding residue
(original residue number in PDB)
E100 D101 E102 R103 K113 R117 G130 G131 S132 K248
Binding residue
(residue number reindexed from 1)
E60 D61 E62 R63 K73 R77 G83 G84 S85 K201
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) E100 G131 S132 Q136
Catalytic site (residue number reindexed from 1) E60 G84 S85 Q89
Enzyme Commision number 2.4.99.28: peptidoglycan glycosyltransferase.
Gene Ontology
Molecular Function
GO:0008658 penicillin binding
GO:0008955 peptidoglycan glycosyltransferase activity
GO:0016757 glycosyltransferase activity
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0046677 response to antibiotic
GO:0071555 cell wall organization
Cellular Component
GO:0005886 plasma membrane

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Molecular Function

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Biological Process

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Cellular Component
External links
PDB RCSB:3vmt, PDBe:3vmt, PDBj:3vmt
PDBsum3vmt
PubMed22493270
UniProtQ99T05|MGT_STAAM Monofunctional glycosyltransferase (Gene Name=mgt)

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