Structure of PDB 4qdi Chain A Binding Site BS02

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 IDUDP
InChIInChI=1S/C9H14N2O12P2/c12-5-1-2-11(9(15)10-5)8-7(14)6(13)4(22-8)3-21-25(19,20)23-24(16,17)18/h1-2,4,6-8,13-14H,3H2,(H,19,20)(H,10,12,15)(H2,16,17,18)/t4-,6-,7-,8-/m1/s1
InChIKeyXCCTYIAWTASOJW-XVFCMESISA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)[C@H]2[C@@H]([C@@H]([C@H](O2)CO[P@@](=O)(O)OP(=O)(O)O)O)O
CACTVS 3.370O[CH]1[CH](O)[CH](O[CH]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
CACTVS 3.370O[C@H]1[C@@H](O)[C@@H](O[C@@H]1CO[P](O)(=O)O[P](O)(O)=O)N2C=CC(=O)NC2=O
OpenEye OEToolkits 1.7.0C1=CN(C(=O)NC1=O)C2C(C(C(O2)COP(=O)(O)OP(=O)(O)O)O)O
ACDLabs 12.01O=P(O)(O)OP(=O)(O)OCC2OC(N1C(=O)NC(=O)C=C1)C(O)C2O
FormulaC9 H14 N2 O12 P2
NameURIDINE-5'-DIPHOSPHATE
ChEMBLCHEMBL130266
DrugBankDB03435
ZINCZINC000004490939
PDB chain4qdi Chain A Residue 502 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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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)		T42 F61 L153
Binding residue
(residue number reindexed from 1)		T34 F53 L145
Annotation score2
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

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

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