Structure of PDB 4qdi Chain A Binding Site BS01

Receptor Information
>4qdi Chain A (length=457) Species: 557600 (Acinetobacter baumannii AB307-0294) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
VPLEPWTAQQLQQATQGYWHKDQIPQTEIKRILTDSRHAESGDAFLALKG
ERFDAHNFVAQVVANGCQVAIVERPIDAEIAQLVVADTRLALGQLGAYRR
EQNAQLKVIALTGSSGKTTTKEMLGSILSRLAPTLITRGNLNNDLGVPMM
LLELRKEHQYAVMELGANHQGEIDYTSKIVQPHVAGILNIGTAHLGEFGG
RDGICRAKSEIYRHILPQGVAIVPQQDDFTAEIREAAKSHQIMSFGEGGD
VFATEIELLPQSANFQLHTPQGSSFVRLPFAGEHNVQNATAAVAFALALG
VSLEDIVKGLEQAQGAKGRLNFIQKAPHLFIDDTYNANPTSMRAAAQVLL
QQNGIKVMVMGDIGELGDSSWQEHHDLGRDLAELPLDHIVAVGQFASAAL
EGAGLHSTKLKAFQTQAEALPFLINLIQTHQPQSMSFLFKGSRFTHMETL
MADLMEK
Ligand information
Ligand IDATP
InChIInChI=1S/C10H16N5O13P3/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(26-10)1-25-30(21,22)28-31(23,24)27-29(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H,23,24)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
InChIKeyZKHQWZAMYRWXGA-KQYNXXCUSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
ACDLabs 10.04O=P(O)(O)OP(=O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
OpenEye OEToolkits 1.5.0c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@@](=O)(O)O[P@](=O)(O)OP(=O)(O)O)O)O)N
CACTVS 3.341Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@](O)(=O)O[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
FormulaC10 H16 N5 O13 P3
NameADENOSINE-5'-TRIPHOSPHATE
ChEMBLCHEMBL14249
DrugBankDB00171
ZINCZINC000004261765
PDB chain4qdi Chain A Residue 501 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
Global viewLocal viewStructure summary

[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
[Spin on] [Spin off] [Reset]
[High quality] [Low quality]
[White background] [Black background]
PDB4qdi ATP-binding mode including a carbamoylated lysine and two Mg(2+) ions, and substrate-binding mode in Acinetobacter baumannii MurF
Resolution1.8 Å
Binding residue
(original residue number in PDB)		S123 G124 K125 T126 T127 H292 N296 R327 Y343 N344
Binding residue
(residue number reindexed from 1)		S115 G116 K117 T118 T119 H284 N288 R319 Y335 N336
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) K125 T126 N148 E172 H202
Catalytic site (residue number reindexed from 1) K117 T118 N140 E164 H194
Enzyme Commision number 6.3.2.10: UDP-N-acetylmuramoyl-tripeptide--D-alanyl-D-alanine ligase.
Gene Ontology
Molecular Function
GO:0005524 ATP binding
GO:0008766 UDP-N-acetylmuramoylalanyl-D-glutamyl-2,6-diaminopimelate-D-alanyl-D-alanine ligase activity
GO:0016874 ligase activity
GO:0016881 acid-amino acid ligase activity
GO:0046872 metal ion binding
GO:0047480 UDP-N-acetylmuramoyl-tripeptide-D-alanyl-D-alanine ligase activity
Biological Process
GO:0008360 regulation of cell shape
GO:0009058 biosynthetic process
GO:0009252 peptidoglycan biosynthetic process
GO:0051301 cell division
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4qdi, PDBe:4qdi, PDBj:4qdi
PDBsum4qdi
PubMed24978312
UniProtA0A0J9X1Z8

[Back to BioLiP]