Structure of PDB 2vd8 Chain A Binding Site BS01

Receptor Information
>2vd8 Chain A (length=387) Species: 198094 (Bacillus anthracis str. Ames) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
EAPFYRDTWVEVDLDAIYNNVTHIKEFIPSDVEIFAVVKGNAYGHDYVPV
AKIALEAGATRLAVAFLDEALVLRRAGITAPILVLGPSPPRDINVAAEND
VALTVFQKEWVDEAIKLWDGSSTMKYHINFDSGMGRIGIRERKELKGFLK
SLEGAPFLELEGVYTHFATADEVETSYFDKQYNTFLEQLSWLKEFGVDPK
FVHTANSAATLRFQGITFNAVRIGIAMYGLSPSVEIRPFLPFKLEPALSL
HTKVAHIKQVIKGDGISYNVTYRTKTEEWIATVAIGYADGWLRRLQGFEV
LVNGKRVPIVGRVTMDQFMIHLPCEVPLGTKVTLIGRQGDEYISATEVAE
YSGTINYEIITTISFRVPRIFIRNGKVVEVINYLNDI
Ligand information
Ligand IDPLP
InChIInChI=1S/C8H10NO6P/c1-5-8(11)7(3-10)6(2-9-5)4-15-16(12,13)14/h2-3,11H,4H2,1H3,(H2,12,13,14)
InChIKeyNGVDGCNFYWLIFO-UHFFFAOYSA-N
SMILES
SoftwareSMILES
CACTVS 3.341Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
OpenEye OEToolkits 1.5.0Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
ACDLabs 10.04O=P(O)(O)OCc1cnc(c(O)c1C=O)C
FormulaC8 H10 N O6 P
NamePYRIDOXAL-5'-PHOSPHATE;
VITAMIN B6 Phosphate
ChEMBLCHEMBL82202
DrugBankDB00114
ZINCZINC000001532514
PDB chain2vd8 Chain A Residue 1041 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB2vd8 Structures of an Alanine Racemase from Bacillus Anthracis (Ba0252) in the Presence and Absence of (R)-1-Aminoethylphosphonic Acid (L-Ala-P).
Resolution1.47 Å
Binding residue
(original residue number in PDB)		K41 Y45 R138 H168 S209 R224 G226 I227 Y359
Binding residue
(residue number reindexed from 1)		K39 Y43 R136 H166 S207 R222 G224 I225 Y357
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K41 R138 H168 R224 Y270 T316 D318
Catalytic site (residue number reindexed from 1) K39 R136 H166 R222 Y268 T314 D316
Enzyme Commision number 5.1.1.1: alanine racemase.
Gene Ontology
Molecular Function
GO:0003824 catalytic activity
GO:0008784 alanine racemase activity
GO:0016853 isomerase activity
GO:0030170 pyridoxal phosphate binding
GO:0046872 metal ion binding
Biological Process
GO:0006522 alanine metabolic process
GO:0009252 peptidoglycan biosynthetic process
GO:0030632 D-alanine biosynthetic process
Cellular Component
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:2vd8, PDBe:2vd8, PDBj:2vd8
PDBsum2vd8
PubMed18453697
UniProtA0A6L7HC45

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