Structure of PDB 1wyu Chain E Binding Site BS01

Receptor Information

>1wyu Chain E (length=437) Species: 300852 (Thermus thermophilus HB8)

MDYTPHTEEEIREMLRRVGAASLEDLFAHLPKEILSPPIDLPEPLPEWKV
LEELRRLAAQNLPAHKAFLGGGVRSHHVPPVVQALAARGEFLTAYTPYQP
EVSQGVLQATFEYQTMIAELAGLEIANASMYDGATALAEGVLLALRETGR
MGVLVSQGVHPEYRAVLRAYLEAVGAKLLTLPLEGGRTPLPEVGEEVGAV
VVQNPNFLGALEDLGPFAEAAHGAGALFVAVADPLSLGVLKPPGAYGADI
AVGDGQSLGLPMGFGGPHFGFLATKKAFVRQLPGRLVSETVDVEGRRGFI
LTLQAREQYIRRAKAKSNITTNAQLTALMGAMYLAALGPEGLREVALKSV
EMAHKLHALLLEVPGVRPFTPKPFFNEFALALPKDPEAVRRALAERGFHG
ATPVPREYGENLALFAATELHEEEDLLALREALKEVL

Ligand information

• Ligand ID: PLP
• InChI: InChI=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)
• InChIKey: NGVDGCNFYWLIFO-UHFFFAOYSA-N
• SMILES:
  CACTVS 3.341: Cc1ncc(CO[P](O)(O)=O)c(C=O)c1O
  OpenEye OEToolkits 1.5.0: Cc1c(c(c(cn1)COP(=O)(O)O)C=O)O
  ACDLabs 10.04: O=P(O)(O)OCc1cnc(c(O)c1C=O)C
• Formula: C8 H10 N O6 P
• Name: PYRIDOXAL-5'-PHOSPHATE;
  VITAMIN B6 Phosphate
• ChEMBL: CHEMBL82202
• DrugBank: DB00114
• ZINC: ZINC000001532514
• PDB chain: 1wyu Chain F Residue 475

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1wyu Structure of P-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): T320 T321
• Binding residue (residue number reindexed from 1): T320 T321
• Annotation score: 1

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

Biological Process

• GO:0006546 glycine catabolic process
• GO:0009116 nucleoside metabolic process
• GO:0019464 glycine decarboxylation via glycine cleavage system

External links

• PDB: RCSB:1wyu, PDBe:1wyu, PDBj:1wyu
• PDBsum: 1wyu
• PubMed: 15791207
• UniProt: Q5SKW8