Structure of PDB 5c3p Chain C Binding Site BS01

Receptor Information

>5c3p Chain C (length=325) Species: 5141 (Neurospora crassa)

MEKAAVNEDGLVIPLIDFSKFLEGDETLKLETAKAILHGFQTAGFIYLKN
IPIQPDFREHVFNTSAKFFKLPKEKKLEVGNRGYSAPGREKVTQLTDPAE
IEKIRSAAPDIKESYEIGREDEPGHPNPWPAEQDDLVGFKSTMNNFFDQC
KALHIEVMRAIAVGMGIDANYFDSFVDVGDNILRLLHYPAVKSEVFKINP
GQVRAGEHTDYGSITLLFQDSRGGLQVKSPNGQFIDATPIENTVVVNAGD
LLARWSNDTIKSTVHRVVEPPKQEDVHPPRYSIAYFCNPNHKSYIEAIPG
TYAAESERKYEGINSGKYLVQRLAA

Ligand information

• Ligand ID: AKG
• InChI: InChI=1S/C5H6O5/c6-3(5(9)10)1-2-4(7)8/h1-2H2,(H,7,8)(H,9,10)
• InChIKey: KPGXRSRHYNQIFN-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04: O=C(O)C(=O)CCC(=O)O
  OpenEye OEToolkits 1.7.6: C(CC(=O)O)C(=O)C(=O)O
  CACTVS 3.385: OC(=O)CCC(=O)C(O)=O
• Formula: C5 H6 O5
• Name: 2-OXOGLUTARIC ACID
• ChEMBL: CHEMBL1686
• DrugBank: DB08845
• ZINC: ZINC000001532519
• PDB chain: 5c3p Chain C Residue 402

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5c3p Molecular basis for the substrate specificity and catalytic mechanism of thymine-7-hydroxylase in fungi
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): R190 Y194 H214 L223 H271 V273 R286 S288 F292
• Binding residue (residue number reindexed from 1): R184 Y188 H208 L217 H265 V267 R280 S282 F286
• Annotation score: 4
• Binding affinity: MOAD: Kd=34.4uM

Enzymatic activity

• Catalytic site (original residue number in PDB): R190 A211 H214 D216 H271
• Catalytic site (residue number reindexed from 1): R184 A205 H208 D210 H265

Gene Ontology

Molecular Function

• GO:0046872 metal ion binding
• GO:0051213 dioxygenase activity

Biological Process

• GO:0044283 small molecule biosynthetic process

External links

• PDB: RCSB:5c3p, PDBe:5c3p, PDBj:5c3p
• PDBsum: 5c3p
• PubMed: 26429971
• UniProt: Q7RYZ9