Structure of PDB 3dxv Chain B Binding Site BS02

Receptor Information
>3dxv Chain B (length=434) Species: 37486 (Achromobacter obae) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KALYDRDGAAIGNLQKLRFFPLAISGGRGARLIEENGRELIDLSGAWGAA
SLGYGHPAIVAAVSAAAANPAGATILSASNAPAVTLAERLLASFPGEGTH
KIWFGHSGSDANEAAYRAIVKATGRSGVIAFAGAYHGCTVGSMAFSGHSV
QADAAKADGLILLPYPDPYRPYRNDPTGDAILTLLTEKLAAVPAGSIGAA
FIEPIQSDGGLIVPPDGFLRKFADICRAHGILVVCDEVKVGLARSGRLHC
FEHEGFVPDILVLGKGLGGGLPLSAVIAPAEILDCASAFAMQTLHGNPIS
AAAGLAVLETIDRDDLPAMAERKGRLLRDGLSELAKRHPLIGDIRGRGLA
CGMELVCDRQSREPARAETAKLIYRAYQLGLVVYYVGMNGNVLEFTPPLT
ITETDIHKALDLLDRAFSELSAVSNEEIAQFAGW
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 chain3dxv Chain B Residue 450 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB3dxv The novel structure of a pyridoxal 5'-phosphate-dependent fold-type I racemase, alpha-amino-epsilon-caprolactam racemase from Achromobacter obae
Resolution2.21 Å
Binding residue
(original residue number in PDB)		S109 S111 Y137 H138 E205 D238 V240 K267
Binding residue
(residue number reindexed from 1)		S107 S109 Y135 H136 E203 D236 V238 K265
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) Q17 Y137 E205 D238 K241 K267 T295 E396
Catalytic site (residue number reindexed from 1) Q15 Y135 E203 D236 K239 K265 T293 E394
Enzyme Commision number 5.1.1.15: 2-aminohexano-6-lactam racemase.
Gene Ontology
Molecular Function
GO:0008453 alanine-glyoxylate transaminase activity
GO:0008483 transaminase activity
GO:0016853 isomerase activity
GO:0030170 pyridoxal phosphate binding
GO:0047463 2-aminohexano-6-lactam racemase activity
Biological Process
GO:0009436 glyoxylate catabolic process
GO:0019481 L-alanine catabolic process, by transamination

View graph for
Molecular Function
View graph for
Biological Process
External links
PDB RCSB:3dxv, PDBe:3dxv, PDBj:3dxv
PDBsum3dxv
PubMed19146406
UniProtQ7M181|ACLR_ACHOB 2-aminohexano-6-lactam racemase

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