Structure of PDB 3hrd Chain A Binding Site BS02

Receptor Information

>3hrd Chain A (length=420) Species: 1528 (Eubacterium barkeri)

GKDYQVLGKNKVKVDSLEKVMGTAKFAADYSFPDMLYAGVFRSTVPHARI
VSLDLSKARAIDGVEAVLDYHAIPGKNRFGIIIKDEPCLVDDKVRRYGDA
IAVVAAQTPDLVQEALDAITIEYEELEGIFTMERALEEDSPAIHGDTNIH
QVKHLEYGDVDAAFKQCDIVVEDTYSTHRLTHMFIEPDAGVSYYDNEGML
TVVVSTQNPHYDRGEVAGMLALPNSKVRIIQATTGGGFGGKLDLSVQCHC
ALLTYHTKKPVKMVRSREESTTVSSKRHPMTMHCKTGATKDGRLQAVQVE
MFGDTGAYASYGPAVITRATVHCMGPYVVPNVRVDAKFVYTNNPMSGAFR
GFGVPQASVCHEGQMNALAKALGMDPIDIRILNAHQVGAKLATGQVLENS
VGLIETLEKAREKAVEVMGY

Ligand information

• Ligand ID: MG
• InChI: InChI=1S/Mg/q+2
• InChIKey: JLVVSXFLKOJNIY-UHFFFAOYSA-N
• SMILES:
  ACDLabs 10.04
  OpenEye OEToolkits 1.5.0: [Mg+2]
  CACTVS 3.341: [Mg++]
• Formula: Mg
• Name: MAGNESIUM ION
• DrugBank: DB01378
• PDB chain: 3hrd Chain A Residue 426

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3hrd The Mo-Se active site of nicotinate dehydrogenase
• Resolution: 2.2 Å
• Binding residue (original residue number in PDB): T207 N209 D213 K242 L243 D244
• Binding residue (residue number reindexed from 1): T206 N208 D212 K241 L242 D243
• Annotation score: 1

Enzymatic activity

• Catalytic site (original residue number in PDB): Q208 L243 R319 H323 R351
• Catalytic site (residue number reindexed from 1): Q207 L242 R318 H322 R350
• Enzyme Commision number: 1.17.1.5: nicotinate dehydrogenase.

Gene Ontology

Molecular Function

• GO:0005506 iron ion binding
• GO:0016491 oxidoreductase activity
• GO:0046872 metal ion binding
• GO:0050138 nicotinate dehydrogenase activity

Biological Process

• GO:1901848 nicotinate catabolic process

External links

• PDB: RCSB:3hrd, PDBe:3hrd, PDBj:3hrd
• PDBsum: 3hrd
• PubMed: 19549881
• UniProt: Q0QLF2|NDLMS_EUBBA Nicotinate dehydrogenase large molybdopterin subunit (Gene Name=ndhL)