Structure of PDB 6h5e Chain B Binding Site BS04

Receptor Information
>6h5e Chain B (length=394) Species: 1280 (Staphylococcus aureus) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DTDVLRKLAEQVDDIVFISGTNGKTTTSNLIGHTLKANNIQIIHNNEGAN
MAAGITSAFIMQSTPKTKIAVIEIDEGSIPRVLKEVTPSMMVFTNFFRDQ
MDRFGEIDIMVNNIAETISNKGIKLLLNADDPFVSRLKIASDTIVYYGMK
AHAHEFEQESRYCPNCGRLLQYDYIHYNQIGHYHCQCGFKREQAKYEISS
FDVAPFLYLNINDEKYDMKIAGDFNAYNALAAYTVLRELGLNEQTIKNGF
ETYTSDNGRMQYFKKERKEAMINLAKNPAGMNASLSVGEQLEGEKVYVIS
LNDNAADGRDTSWIYDADFEKLSKQQIEAIIVTGTRAEELQLRLKLAEVE
VPIIVERDIYKATAKTMDYKGFTVAIPNYTSLAPMLEQLNRSFE
Ligand information
Ligand IDANP
InChIInChI=1S/C10H17N6O12P3/c11-8-5-9(13-2-12-8)16(3-14-5)10-7(18)6(17)4(27-10)1-26-31(24,25)28-30(22,23)15-29(19,20)21/h2-4,6-7,10,17-18H,1H2,(H,24,25)(H2,11,12,13)(H4,15,19,20,21,22,23)/t4-,6-,7-,10-/m1/s1
InChIKeyPVKSNHVPLWYQGJ-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(NP(=O)(O)O)O)O)O)N
CACTVS 3.370Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[CH](O)[CH]3O
CACTVS 3.370Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P](O)(=O)O[P](O)(=O)N[P](O)(O)=O)[C@@H](O)[C@H]3O
ACDLabs 12.01O=P(O)(O)NP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.7.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)O[P@@](=O)(NP(=O)(O)O)O)O)O)N
FormulaC10 H17 N6 O12 P3
NamePHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER
ChEMBLCHEMBL1230989
DrugBank
ZINCZINC000008660410
PDB chain6h5e Chain D Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

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PDB6h5e Structural basis of cell wall peptidoglycan amidation by the GatD/MurT complex of Staphylococcus aureus.
Resolution2.139 Å
Binding residue
(original residue number in PDB)		M136 D137
Binding residue
(residue number reindexed from 1)		M101 D102
Annotation score3
Enzymatic activity
Enzyme Commision number 6.3.5.13: lipid II isoglutaminyl synthase (glutamine-hydrolyzing).
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008270 zinc ion binding
GO:0016874 ligase activity
GO:0016879 ligase activity, forming carbon-nitrogen bonds
GO:0016881 acid-amino acid ligase activity
GO:0046872 metal ion binding
GO:0140282 carbon-nitrogen ligase activity on lipid II
Biological Process
GO:0008360 regulation of cell shape
GO:0009058 biosynthetic process
GO:0009252 peptidoglycan biosynthetic process
GO:0071555 cell wall organization

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:6h5e, PDBe:6h5e, PDBj:6h5e
PDBsum6h5e
PubMed30154570
UniProtA0A0H3JUU7|MURT_STAAN Lipid II isoglutaminyl synthase (glutamine-hydrolyzing) subunit MurT (Gene Name=murT)

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