Structure of PDB 1gde Chain B Binding Site BS01

Receptor Information

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

ALSDRLELVSASEIRKLFDIAAGMKDVISLGIGEPDFDTPQHIKEYAKEA
LDKGLTHYGPNIGLLELREAIAEKLKKQNGIEADPKTEIMVLLGANQAFL
MGLSAFLKDGEEVLIPTPAFVSYAPAVILAGGKPVEVPTYEEDEFRLNVD
ELKKYVTDKTRALIINSPCNPTGAVLTKKDLEEIADFVVEHDLIVISDEV
YEHFIYDDARHYSIASLDGMFERTITVNGFSKTFAMTGWRLGFVAAPSWI
IERMVKFQMYNATCPVTFIQYAAAKALKDERSWKAVEEMRKEYDRRRKLV
WKRLNEMGLPTVKPKGAFYIFPRIRDTGLTSKKFSELMLKEARVAVVPGS
AFGKAGEGYVRISYATAYEKLEEAMDRMERVLKERKLV

Ligand information

• Ligand ID: GLU
• InChI: InChI=1S/C5H9NO4/c6-3(5(9)10)1-2-4(7)8/h3H,1-2,6H2,(H,7,8)(H,9,10)/t3-/m0/s1
• InChIKey: WHUUTDBJXJRKMK-VKHMYHEASA-N
• SMILES:
  ACDLabs 12.01: O=C(O)C(N)CCC(=O)O
  OpenEye OEToolkits 1.7.0: C(CC(=O)O)C(C(=O)O)N
  OpenEye OEToolkits 1.7.0: C(CC(=O)O)[C@@H](C(=O)O)N
  CACTVS 3.370: N[C@@H](CCC(O)=O)C(O)=O
  CACTVS 3.370: N[CH](CCC(O)=O)C(O)=O
• Formula: C5 H9 N O4
• Name: GLUTAMIC ACID
• ChEMBL: CHEMBL575060
• DrugBank: DB00142
• ZINC: ZINC000001482113
• PDB chain: 1gde Chain A Residue 914

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): G534 F621 N671 Y820
• Binding residue (residue number reindexed from 1): G33 F120 N170 Y319
• 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