Structure of PDB 7nbd Chain DDD Binding Site BS02

Receptor Information
>7nbd Chain DDD (length=318) Species: 9606 (Homo sapiens) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
QYDISFADVEKAHINIRDSIHLTPVLTSSILNQLTGRNLFFKCELFQKTG
SFKIRGALNAVRSLVRKPKAVVTHSSGNHGQALTYAAKLEGIPAYIVVPQ
TAPDCKKLAIQAYGASIVYCEPSDESRENVAKRVTEETEGIMVHPNQEPA
VIAGQGTIALEVLNQVPLVDALVVPVGGGGMLAGIAITVKALKPSVKVYA
AEPSNADDCYQSKLKGKLMPNLYPPETIADGVKSSIGLNTWPIIRDLVDD
IFTVTEDEIKCATQLVWERMKLLIEPTAGVGVAAVLSQHFQTVSPEVKNI
CIVLSGGNVDLTSSITWV
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 chain7nbd Chain DDD Residue 401 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB7nbd Tyrosine 121 moves revealing a ligandable pocket that couples catalysis to ATP-binding in serine racemase.
Resolution1.865 Å
Binding residue
(original residue number in PDB)		F55 K56 N86 G185 G186 G187 G188 M189 G239 V240 E283 T285 S313 G314
Binding residue
(residue number reindexed from 1)		F52 K53 N78 G177 G178 G179 G180 M181 G231 V232 E275 T277 S305 G306
Annotation score1
Enzymatic activity
Catalytic site (original residue number in PDB) K56 S84 E210 A214 D216 G239 L312 S313
Catalytic site (residue number reindexed from 1) K53 S76 E202 A206 D208 G231 L304 S305
Enzyme Commision number 4.3.1.17: L-serine ammonia-lyase.
4.3.1.18: D-serine ammonia-lyase.
5.1.1.18: serine racemase.
Gene Ontology
Molecular Function
GO:0000287 magnesium ion binding
GO:0003824 catalytic activity
GO:0003941 L-serine ammonia-lyase activity
GO:0005509 calcium ion binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0008721 D-serine ammonia-lyase activity
GO:0016594 glycine binding
GO:0016829 lyase activity
GO:0016853 isomerase activity
GO:0018114 threonine racemase activity
GO:0030165 PDZ domain binding
GO:0030170 pyridoxal phosphate binding
GO:0030378 serine racemase activity
GO:0042802 identical protein binding
GO:0042803 protein homodimerization activity
GO:0046872 metal ion binding
Biological Process
GO:0006520 amino acid metabolic process
GO:0006563 L-serine metabolic process
GO:0009069 serine family amino acid metabolic process
GO:0009410 response to xenobiotic stimulus
GO:0014070 response to organic cyclic compound
GO:0032496 response to lipopolysaccharide
GO:0042866 pyruvate biosynthetic process
GO:0070178 D-serine metabolic process
GO:0070179 D-serine biosynthetic process
Cellular Component
GO:0005737 cytoplasm
GO:0005829 cytosol
GO:0043025 neuronal cell body
GO:0045177 apical part of cell

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:7nbd, PDBe:7nbd, PDBj:7nbd
PDBsum7nbd
PubMed35410329
UniProtQ9GZT4|SRR_HUMAN Serine racemase (Gene Name=SRR)

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