Structure of PDB 1wyv Chain F Binding Site BS01

Receptor Information
>1wyv Chain F (length=473) Species: 300852 (Thermus thermophilus HB8) [Search protein sequence] [Download receptor structure] [Download structure with residue number starting from 1] [View receptor structure]
SFPLIFERSRKGRRGLKLVKAVPKAEDLIPKEHLREVPPRLPEVDELTLV
RHYTGLSRRQVGVDTTFYPLGSCTMKYNPKLHEEAARLFADLHPYQDPRT
AQGALRLMWELGEYLKALTGMDAITLEPAAGAHGELTGILIIRAYHEDRG
EGRTRRVVLVPDSAHGSNPATASMAGYQVREIPSGPEGEVDLEALKRELG
PHVAALMLTNPNTLGLFERRILEISRLCKEAGVQLYYDGANLNAIMGWAR
PGDMGFDVVHLNLHKTFTVPHGGGGPGSGPVGVKAHLAPYLPVPLVERGE
EGFYLDFDRPKSIGRVRSFYGNFLALVRAWAYIRTLGLEGLKKAAALAVL
NARYLKELLKEKGYRVPYDGPSMHEFVAQPPEGFRALDLAKGLLELGFHP
PTVYFPLIVKEALMVEPTETEAKETLEAFAEAMGALLKKPKEWLENAPYS
TPVRRLDELRANKHPKLTYFDEG
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 chain1wyv Chain F Residue 3475 [Download ligand structure] [Download structure with residue number starting from 1] [View ligand structure]
Receptor-Ligand Complex Structure
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PDB1wyv Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia
Resolution2.4 Å
Binding residue
(original residue number in PDB)		S73 G132 A133 H166 D239 A241 N263 H265 K266
Binding residue
(residue number reindexed from 1)		S72 G131 A132 H165 D238 A240 N262 H264 K265
Annotation score1
Enzymatic activity
Enzyme Commision number 1.4.4.2: glycine dehydrogenase (aminomethyl-transferring).
Gene Ontology
Molecular Function
GO:0004375 glycine dehydrogenase (decarboxylating) activity
GO:0016491 oxidoreductase activity
GO:0016594 glycine binding
GO:0030170 pyridoxal phosphate binding
Biological Process
GO:0006546 glycine catabolic process
GO:0019464 glycine decarboxylation via glycine cleavage system
Cellular Component
GO:0005829 cytosol
GO:0005960 glycine cleavage complex

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Molecular Function
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Biological Process
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Cellular Component
External links
PDB RCSB:1wyv, PDBe:1wyv, PDBj:1wyv
PDBsum1wyv
PubMed15791207
UniProtQ5SKW7|GCSPB_THET8 Probable glycine dehydrogenase (decarboxylating) subunit 2 (Gene Name=gcvPB)

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