Structure of PDB 5a88 Chain D Binding Site BS01

Receptor Information

>5a88 Chain D (length=137) Species: 1697 (Corynebacterium ammoniagenes)

HFYVTGPVVRGGFPTANQYFHDTVALPADGVYAGWLTILPTEAPVSGNME
PEVAYAAAISVGTNQRSVESFVLDRDADLYGHDVKVEFVDHVRAMEKFDS
VEQLLEVMAKDVQKTRTLLAQDVQAHKMAPETYFLQA

Ligand information

• Ligand ID: ADP
• InChI: InChI=1S/C10H15N5O10P2/c11-8-5-9(13-2-12-8)15(3-14-5)10-7(17)6(16)4(24-10)1-23-27(21,22)25-26(18,19)20/h2-4,6-7,10,16-17H,1H2,(H,21,22)(H2,11,12,13)(H2,18,19,20)/t4-,6-,7-,10-/m1/s1
• InChIKey: XTWYTFMLZFPYCI-KQYNXXCUSA-N
• SMILES:
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)[C@H]3[C@@H]([C@@H]([C@H](O3)CO[P@](=O)(O)OP(=O)(O)O)O)O)N
  CACTVS 3.341: Nc1ncnc2n(cnc12)[CH]3O[CH](CO[P](O)(=O)O[P](O)(O)=O)[CH](O)[CH]3O
  ACDLabs 10.04: O=P(O)(O)OP(=O)(O)OCC3OC(n2cnc1c(ncnc12)N)C(O)C3O
  CACTVS 3.341: Nc1ncnc2n(cnc12)[C@@H]3O[C@H](CO[P@@](O)(=O)O[P](O)(O)=O)[C@@H](O)[C@H]3O
  OpenEye OEToolkits 1.5.0: c1nc(c2c(n1)n(cn2)C3C(C(C(O3)COP(=O)(O)OP(=O)(O)O)O)O)N
• Formula: C10 H15 N5 O10 P2
• Name: ADENOSINE-5'-DIPHOSPHATE
• ChEMBL: CHEMBL14830
• DrugBank: DB16833
• ZINC: ZINC000012360703
• PDB chain: 5a88 Chain D Residue 501

Receptor-Ligand Complex Structure

Structure summary

• PDB: 5a88 Structural Insights Into the Synthesis of Fmn in Prokaryotic Organisms.
• Resolution: 2.08 Å
• Binding residue (original residue number in PDB): G196 T208 N210 V271 R274 D275 A276 L278 Y279
• Binding residue (residue number reindexed from 1): G11 T15 N17 V72 R75 D76 A77 L79 Y80
• Annotation score: 5

Enzymatic activity

• Enzyme Commision number: 2.7.1.26: riboflavin kinase.
  2.7.7.2: FAD synthase.

Gene Ontology

Molecular Function

• GO:0008531 riboflavin kinase activity

Biological Process

• GO:0009231 riboflavin biosynthetic process

External links

• PDB: RCSB:5a88, PDBe:5a88, PDBj:5a88
• PDBsum: 5a88
• PubMed: 26627660
• UniProt: Q59263|RIBF_CORAM Bifunctional riboflavin kinase/FMN adenylyltransferase (Gene Name=ribF)