Structure of PDB 4cvk Chain A Binding Site BS02

Receptor Information
>4cvk Chain A (length=438) Species: 208964 (Pseudomonas aeruginosa PAO1) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
MLEPLRLSQLTVALDARLIGEDAVFSAVSTDSRAIGPGELFIALSGPRFD
GHDYLAEVAAKGAVAALVEREVAAPLPQLLVRDTRAALGRLGALNRRKFT
GPLAAMTGSSGKTTVKEMLASILRTQAGDAESVLATRGNLNNDLGVPLTL
LQLAPQHRSAVIELGASRIGEIAYTVELTRPHVAIITNAFGGPEKIVEAK
GEILEGLAADGTAVLNLDDKAFDTWKARASGRPLLTFSLDRPQADFRAAD
LQRDARGCMGFRLQGVAGEAQVQLNLLGRHNVANALAAAAAAHALGVPLD
GIVAGLQALQPVKGRAVAQLTASGLRVIDDSYNANPASMLAAIDILSGFS
GRTVLVLGDMGAEQAHREVGAYAAGKVSALYAVGPLMAHAVQAFGATGRH
FADQASLIGALATEDPTTTILIKGSRSAAMDKVVAALC
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 chain4cvk Chain A Residue 1452 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB4cvk Pamurf in Complex with Udp-Murnac-Tripeptide (Mdap)
Resolution1.92 Å
Binding residue
(original residue number in PDB)		T30 D31 S32 R33 L44 G46 P47 R48 F49 Y54
Binding residue
(residue number reindexed from 1)		T30 D31 S32 R33 L44 G46 P47 R48 F49 Y54
Annotation score2
Enzymatic activity
Catalytic site (original residue number in PDB) K113 T114 D144 E164
Catalytic site (residue number reindexed from 1) K112 T113 D143 E163
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:4cvk, PDBe:4cvk, PDBj:4cvk
PDBsum4cvk
PubMed
UniProtQ9HVZ7

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