Structure of PDB 6h5e Chain D Binding Site BS02

Receptor Information
>6h5e Chain D (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
AHAHEFEESRYCPNCGRLLQYDYIHYNQIGHYHCQCGFKREQAKYEISSF
DVAPFLYLNINDEKYDMKIAGDFNAYNALAAYTVLRELGLNEQTIKNGFE
TYTSDNGRMQYFKKERKEAMINLAKNPAGMNASLSVGEQLEGEKVYVISL
NDNAADGRDTSWIYDADFEKLSKQQIEAIIVTGTRAEELQLRLKLAEVEV
PIIVERDIYKATAKTMDYKGFTVAIPNYTSLAPMLEQLNRSFEG
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)		N57 G58 K59 T60 E108 N130 F132 Y216 F263 N267
Binding residue
(residue number reindexed from 1)		N22 G23 K24 T25 E73 N95 F97 Y176 F223 N227
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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