Structure of PDB 4c5a Chain B Binding Site BS04

Receptor Information
>4c5a Chain B (length=304) Species: 83333 (Escherichia coli K-12) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
DKIAVLLGGTSAEREVSLNSGAAVLAGLREGGIDAYPVDPKEVDVTQLKS
MGFQKVFIALHGRGGEDGTLQGMLELMGLPYTGSGVMASALSMDKLRSKL
LWQGAGLPVAPWVALTRAEFEKGLSDKQLAEISALGLPVIVKPSREGSSV
GMSKVVAENALQDALRLAFQHDEEVLIEKWLSGPEFTVAILGEEILPSIR
IQPSGTFYDYEAKYLSDETQYFCPAGLEASQEANLQALVLKAWTTLGCKG
WGRIDVMLDSDGQFYLLEANTSPGMTSHSLVPMAARQAGMSFSQLVVRIL
ELAD
Ligand information
Ligand IDMG
InChIInChI=1S/Mg/q+2
InChIKeyJLVVSXFLKOJNIY-UHFFFAOYSA-N
SMILES
SoftwareSMILES
ACDLabs 10.04
OpenEye OEToolkits 1.5.0		[Mg+2]
CACTVS 3.341[Mg++]
FormulaMg
NameMAGNESIUM ION
ChEMBL
DrugBankDB01378
ZINC
PDB chain4c5a Chain B Residue 331 [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]
PDB4c5a Inhibition of D-Ala:D-Ala ligase through a phosphorylated form of the antibiotic D-cycloserine.
Resolution1.65 Å
Binding residue
(original residue number in PDB)		D257 E270
Binding residue
(residue number reindexed from 1)		D255 E268
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) E15 V18 N21 H63 S150 E213 Y216 R255 D257 E270 N272 G276 H280
Catalytic site (residue number reindexed from 1) E13 V16 N19 H61 S148 E211 Y214 R253 D255 E268 N270 G274 H278
Enzyme Commision number 6.3.2.4: D-alanine--D-alanine ligase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0005524 ATP binding
GO:0008716 D-alanine-D-alanine ligase activity
GO:0016874 ligase activity
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0008360 regulation of cell shape
GO:0009252 peptidoglycan biosynthetic process
GO:0071555 cell wall organization
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol

View graph for
Molecular Function
View graph for
Biological Process
View graph for
Cellular Component
External links
PDB RCSB:4c5a, PDBe:4c5a, PDBj:4c5a
PDBsum4c5a
PubMed29208891
UniProtP07862|DDLB_ECOLI D-alanine--D-alanine ligase B (Gene Name=ddlB)

[Back to BioLiP]