Structure of PDB 3hrd Chain A

Receptor sequence

>3hrdA (length=420) Species: 1528 (Eubacterium barkeri)

GKDYQVLGKNKVKVDSLEKVMGTAKFAADYSFPDMLYAGVFRSTVPHARI
VSLDLSKARAIDGVEAVLDYHAIPGKNRFGIIIKDEPCLVDDKVRRYGDA
IAVVAAQTPDLVQEALDAITIEYEELEGIFTMERALEEDSPAIHGDTNIH
QVKHLEYGDVDAAFKQCDIVVEDTYSTHRLTHMFIEPDAGVSYYDNEGML
TVVVSTQNPHYDRGEVAGMLALPNSKVRIIQATTGGGFGGKLDLSVQCHC
ALLTYHTKKPVKMVRSREESTTVSSKRHPMTMHCKTGATKDGRLQAVQVE
MFGDTGAYASYGPAVITRATVHCMGPYVVPNVRVDAKFVYTNNPMSGAFR
GFGVPQASVCHEGQMNALAKALGMDPIDIRILNAHQVGAKLATGQVLENS
VGLIETLEKAREKAVEVMGY

3D structure

• PDB: 3hrd The Mo-Se active site of nicotinate dehydrogenase
• Chain: A
• Resolution: 2.2 Å

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.

Interaction with ligand

Site #	Ligand	Ligand chain	Binding residues on receptor (original residue number in PDB)	Binding residues on receptor (residue number reindexed from 1)	Binding affinity
BS01	SE	A	F239 G240 A349 F350 R351	F238 G239 A348 F349 R350
BS02	MG	A	T207 N209 D213 K242 L243 D244	T206 N208 D212 K241 L242 D243
BS03	MG	A	T306 Y309 A310 S347	T305 Y308 A309 S346
BS04	MCN	A	G237 G238 F239 R351	G236 G237 F238 R350
BS05	NIO	A	A315 R319 F353	A314 R318 F352

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)