Structure of PDB 8rb8 Chain D Binding Site BS01

Receptor Information

>8rb8 Chain D (length=349) Species: 322710 (Azotobacter vinelandii DJ)

SVAAGPFAHDRSSVNRIMLDVCLALTPATLFGLVMFGWPAINLWLVTCVS
ALAIEAACLRLLGQPMRRLLDGSALLTGWLLAISLPPWAPWWIGVGGSLF
AIGIGKQLYGGIGQNPFNPAMLARVALLIAFPLQMTTWALPHPLFSSSAP
GFFDSLAITFAGAPLADGMTGATALGNLKTELTLNRTAQEILEGGFSTIS
ALFGSTPGSLGETSELLLLVGGVWLVLRRIIHWEIPVAILASVFVMATLA
YLINPERYAGGLYQLTSGGLILCAFFIATDPVTSPISRVGRLIFGVGCGV
LIYVIRTWGSFPEAAAFAVLFMNALTPLIDRYWRPRAYGRNVRGKPLVA

Ligand information

• Ligand ID: RBF
• InChI: InChI=1S/C17H20N4O6/c1-7-3-9-10(4-8(7)2)21(5-11(23)14(25)12(24)6-22)15-13(18-9)16(26)20-17(27)19-15/h3-4,11-12,14,22-25H,5-6H2,1-2H3,(H,20,26,27)/t11-,12+,14-/m0/s1
• InChIKey: AUNGANRZJHBGPY-SCRDCRAPSA-N
• SMILES:
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[CH](O)[CH](O)[CH](O)CO)c2cc1C
  OpenEye OEToolkits 1.7.6: Cc1cc2c(cc1C)N(C3=NC(=O)NC(=O)C3=N2)CC(C(C(CO)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](CO)O)O)O
  CACTVS 3.385: Cc1cc2N=C3C(=O)NC(=O)N=C3N(C[C@H](O)[C@H](O)[C@H](O)CO)c2cc1C
  ACDLabs 12.01: N=2C(=O)NC(=O)C3=Nc1cc(C)c(C)cc1N(C=23)CC(O)C(O)C(O)CO
• Formula: C17 H20 N4 O6
• Name: RIBOFLAVIN;
  RIBOFLAVINE;
  VITAMIN B2
• ChEMBL: CHEMBL1534
• DrugBank: DB00140
• ZINC: ZINC000002036848
• PDB chain: 8rb8 Chain D Residue 403

Receptor-Ligand Complex Structure

Structure summary

• PDB: 8rb8 Architecture of the RNF1 complex that drives biological nitrogen fixation.
• Resolution: 3.41 Å
• Binding residue (original residue number in PDB): M22 L80 T81 L84 N119 N122 P123 A124 F280 I281 T283 D284 P285 V286
• Binding residue (residue number reindexed from 1): M18 L76 T77 L80 N115 N118 P119 A120 F276 I277 T279 D280 P281 V282
• Annotation score: 4

Gene Ontology

Biological Process

• GO:0022900 electron transport chain

Cellular Component

• GO:0005886 plasma membrane

External links

• PDB: RCSB:8rb8, PDBe:8rb8, PDBj:8rb8
• PDBsum: 8rb8
• PubMed: 38890433
• UniProt: C1DMA5