Structure of PDB 6qkb Chain A Binding Site BS01

Receptor Information
>6qkb Chain A (length=384) Species: 266 (Paracoccus denitrificans) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
KTDFSGYEVGYDIPALPGMDESEIQTPCLILDLDALERNIRKMGDYAKAH
GMRHRSHGKMHKSVDVQKLQESLGGSVGVCCQKVSEAEAFARGGIKDVLV
TNEVREPAKIDRLARLPKTGATVTVCVDDVQNIADLSAAAQKHGTELGIF
VEIDCGAGRCGVTTKEAVVEIAKAAAAAPNLTFKGIQAYQGAMQHMDSFE
DRKAKLDAAIAQVKEAVDALEAEGLAPEFVSGGGTGSYYFESNSGIYNEL
QCGSYAFMDADYGRIHDAEGKRIDQGEWENALFILTSVMSHAKPHLAVVD
AGLKAQSVDSGLPFVYGRDDVKYIKCSDEHGVVEDKDGVLKVNDKLRLVP
GHCDPTCNVHDWYVGVRNGKVETVWPVSARGKGY
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 chain6qkb Chain A Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB6qkb Marine Proteobacteria metabolize glycolate via the beta-hydroxyaspartate cycle.
Resolution1.701 Å
Binding residue
(original residue number in PDB)		H60 K62 Q85 Y192 T238 Q254 G256 S257 Y265
Binding residue
(residue number reindexed from 1)		H57 K59 Q82 Y189 T235 Q251 G253 S254 Y262
Annotation score1
Enzymatic activity
Enzyme Commision number 4.1.3.41: 3-hydroxy-D-aspartate aldolase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0008721 D-serine ammonia-lyase activity
GO:0016829 lyase activity
GO:0016833 oxo-acid-lyase activity
GO:0030170 pyridoxal phosphate binding
GO:0046872 metal ion binding
Biological Process
GO:0009436 glyoxylate catabolic process
GO:0036088 D-serine catabolic process
GO:0046296 glycolate catabolic process

View graph for
Molecular Function
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Biological Process
External links
PDB RCSB:6qkb, PDBe:6qkb, PDBj:6qkb
PDBsum6qkb
PubMed31723261
UniProtA1B8Z1|BHCC_PARDP 3-hydroxy-D-aspartate aldolase (Gene Name=bhcC)

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