Structure of PDB 6rfr Chain B Binding Site BS02

Receptor Information

>6rfr Chain B (length=456) Species: 4952 (Yarrowia lipolytica)

RQYGGLKDQDRIFQNLYDNYGWDLASARKQGDWYKTKELILKGDTWIIDE
IKKSGLRGRGGAGFPSGLKWSFMNPPGWEKNEGPRYLVVNADEGEPGTCK
DREIMRKDPHKLVEGCLLAGRAMNATAAYIYIRGEFYNEAAVLQTAINEA
YAAGLIGKDACGSGYDFDVYIHRGMGAYVCGEETSLIESLEGKAGKPRLK
PPFPAGVGLFGRPSTVTNVETVAVAPTILRRGGDWFASFGRERNSGTKLF
CISGNVNEPCTVEEEMSIPLRELLEKHCGGIKGGWDNLLGVIPGGCSVPI
LPKNICEDVLMDFDALKDVQSGLGTAAVIVINKQQDVIRAIQRFAAFYKH
ESCGQCTPCREGTTWLLKAMDRFRTGQAKEREIDMLYELTKDIEGHTICA
LGDAAAWPIQGLIRNFRPEMETRMKKFHDEVGAVSVGGWMKDARVEKGKV
VGAPLP

Ligand information

• Ligand ID: FMN
• InChI: InChI=1S/C17H21N4O9P/c1-7-3-9-10(4-8(7)2)21(15-13(18-9)16(25)20-17(26)19-15)5-11(22)14(24)12(23)6-30-31(27,28)29/h3-4,11-12,14,22-24H,5-6H2,1-2H3,(H,20,25,26)(H2,27,28,29)/t11-,12+,14-/m0/s1
• InChIKey: FVTCRASFADXXNN-SCRDCRAPSA-N
• SMILES:
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(COP(=O)(O)O)O)O)O
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)C[C@@H]([C@@H]([C@@H](COP(=O)(O)O)O)O)O
  ACDLabs 12.01: N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)COP(=O)(O)O
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO[P](O)(O)=O)c2cc1C
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO[P](O)(O)=O)c2cc1C
• Formula: C17 H21 N4 O9 P
• Name: FLAVIN MONONUCLEOTIDE;
  RIBOFLAVIN MONOPHOSPHATE
• ChEMBL: CHEMBL1201794
• DrugBank: DB03247
• ZINC: ZINC000003831425
• PDB chain: 6rfr Chain B Residue 502

Receptor-Ligand Complex Structure

Structure summary

• PDB: 6rfr High-resolution cryo-EM structures of respiratory complex I: Mechanism, assembly, and disease.
• Resolution: 3.2 Å
• Binding residue (original residue number in PDB): G86 G88 K97 N118 D120 E123 G209 E210 T245 N246 A428 L429
• Binding residue (residue number reindexed from 1): G58 G60 K69 N90 D92 E95 G181 E182 T217 N218 A400 L401
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 7.1.1.2: NADH:ubiquinone reductase (H(+)-translocating).

Gene Ontology

Molecular Function

• GO:0008137 NADH dehydrogenase (ubiquinone) activity
• GO:0010181 FMN binding
• GO:0046872 metal ion binding
• GO:0051287 NAD binding
• GO:0051539 4 iron, 4 sulfur cluster binding

Biological Process

• GO:1902600 proton transmembrane transport

Cellular Component

• GO:0005739 mitochondrion
• GO:0005743 mitochondrial inner membrane
• GO:0045271 respiratory chain complex I

External links

• PDB: RCSB:6rfr, PDBe:6rfr, PDBj:6rfr
• PDBsum: 6rfr
• PubMed: 31844670
• UniProt: F2Z660