Structure of PDB 5nri Chain A Binding Site BS02

Receptor Information
>5nri Chain A (length=311) Species: 357348 (Burkholderia pseudomallei 1106a) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SGIDPKRFGKVAVLLGGDSAEREVSLNSGRLVLQGLRDAGIDAHPFDPAQ
RPLAALKDEGFVRAFNALHGGYGENGQIQGALDFYGIRYTGSGVLGSALG
LDKFRTKLVWQQTGIPTPPFETVMRGDDYAARAQDIVAKLGVPLFVKPAS
EGSSVAVEKVKSADALPAALEEAAKHDKIVIVEKSIEGGGEYTACIAADL
DLPLIRIVPAGEFYDYHAKYIANDTQYLIPCGLDAAKEAEFKRIARRAFD
VLGCTDWGRADFMLDAAGNPYFLEVNTAPGMTDHSLPPKAARAVGIGYSE
LVVKVLSLTLD
Ligand information
Ligand IDDAL
InChIInChI=1S/C3H7NO2/c1-2(4)3(5)6/h2H,4H2,1H3,(H,5,6)/t2-/m1/s1
InChIKeyQNAYBMKLOCPYGJ-UWTATZPHSA-N
SMILES
SoftwareSMILES
OpenEye OEToolkits 1.5.0CC(C(=O)O)N
CACTVS 3.341C[CH](N)C(O)=O
CACTVS 3.341C[C@@H](N)C(O)=O
ACDLabs 10.04O=C(O)C(N)C
OpenEye OEToolkits 1.5.0C[C@H](C(=O)O)N
FormulaC3 H7 N O2
NameD-ALANINE
ChEMBLCHEMBL66693
DrugBankDB01786
ZINCZINC000004658556
PDB chain5nri Chain A Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5nri Burkholderia pseudomallei d-alanine-d-alanine ligase; detailed characterisation and assessment of a potential antibiotic drug target.
Resolution1.5 Å
Binding residue
(original residue number in PDB)		R260 S286 L287
Binding residue
(residue number reindexed from 1)		R259 S285 L286
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) V25 N28 H70 H218 R260 G281 H285
Catalytic site (residue number reindexed from 1) V24 N27 H69 H217 R259 G280 H284
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: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

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:5nri, PDBe:5nri, PDBj:5nri
PDBsum5nri
PubMed31260169
UniProtA3NZL3|DDL_BURP0 D-alanine--D-alanine ligase (Gene Name=ddl)

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