Structure of PDB 1gde Chain B Binding Site BS02

Receptor Information

>1gde Chain B (length=388) Species: 53953 (Pyrococcus horikoshii)

ALSDRLELVSASEIRKLFDIAAGMKDVISLGIGEPDFDTPQHIKEYAKEA
LDKGLTHYGPNIGLLELREAIAEKLKKQNGIEADPKTEIMVLLGANQAFL
MGLSAFLKDGEEVLIPTPAFVSYAPAVILAGGKPVEVPTYEEDEFRLNVD
ELKKYVTDKTRALIINSPCNPTGAVLTKKDLEEIADFVVEHDLIVISDEV
YEHFIYDDARHYSIASLDGMFERTITVNGFSKTFAMTGWRLGFVAAPSWI
IERMVKFQMYNATCPVTFIQYAAAKALKDERSWKAVEEMRKEYDRRRKLV
WKRLNEMGLPTVKPKGAFYIFPRIRDTGLTSKKFSELMLKEARVAVVPGS
AFGKAGEGYVRISYATAYEKLEEAMDRMERVLKERKLV

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: 1gde Chain B Residue 913

Receptor-Ligand Complex Structure

Structure summary

• PDB: 1gde Temperature dependence of the enzyme-substrate recognition mechanism.
• Resolution: 1.8 Å
• Binding residue (original residue number in PDB): G595 A596 N597 F621 N667 D699 Y702 S732 K733 R741
• Binding residue (residue number reindexed from 1): G94 A95 N96 F120 N166 D198 Y201 S231 K232 R240
• Annotation score: 4

Enzymatic activity

• Catalytic site (original residue number in PDB): F621 D699 V701 K733
• Catalytic site (residue number reindexed from 1): F120 D198 V200 K232
• Enzyme Commision number: 2.6.1.-

Gene Ontology

Molecular Function

• GO:0003824 catalytic activity
• GO:0008483 transaminase activity
• GO:0030170 pyridoxal phosphate binding

Biological Process

• GO:0006520 amino acid metabolic process
• GO:0009058 biosynthetic process

External links

• PDB: RCSB:1gde, PDBe:1gde, PDBj:1gde
• PDBsum: 1gde
• PubMed: 11134972
• UniProt: O59096