Structure of PDB 5c1p Chain D Binding Site BS02

Receptor Information
>5c1p Chain D (length=302) Species: 632 (Yersinia pestis) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
AEKVAVLLGGTSAEREVSLLSGQAVLAGLKEAGIDAYGVDTKDFPVTQLK
EQGFDKVFIALHGRGGEDGTLQGVLEFLQLPYTGSGVMASALTMDKLRTK
LVWQALGLPISPYVALNRQQFETLSPEELVACVAKLGLPLIVKPSHEVGM
SKVDHASELQKALVEAFQHDSDVLIEKWLSGPEFTVAILGDEVLPSIRIQ
PPGVFYDYDAKYLSDKTQYFCPSGLSDESEQQLAALALQAYHALDCSGWG
RVDVMQDRDGHFYLLEVNTSPGMTSHSLVPMAARQYGLSFSQLVARILML
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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 chain5c1p Chain D Residue 402 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB5c1p Structure of D-alanine-D-alanine ligase from Yersinia pestis: nucleotide phosphate recognition by the serine loop.
Resolution2.4 Å
Binding residue
(original residue number in PDB)		Y216 R255 N272 P275 G276
Binding residue
(residue number reindexed from 1)		Y212 R251 N268 P271 G272
Annotation score5
Enzymatic activity
Catalytic site (original residue number in PDB) E15 V18 L21 H63 D213 Y216 R255 D257 E270 N272 G276 H280
Catalytic site (residue number reindexed from 1) E14 V17 L20 H62 D209 Y212 R251 D253 E266 N268 G272 H276
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:5c1p, PDBe:5c1p, PDBj:5c1p
PDBsum5c1p
PubMed26894530
UniProtQ8ZIE7|DDL_YERPE D-alanine--D-alanine ligase (Gene Name=ddl)

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