Structure of PDB 7uf5 Chain A Binding Site BS01

Receptor Information

>7uf5 Chain A (length=208) Species: 666 (Vibrio cholerae)

NQSSLLAEFGDPITRVENALQALREGRGVLLLDDEDRENEGDIIYAVESL
TTAQMALMIRECSGIVCLCLTEAQADRLALPPMVVAFTVSIEAKHGVTTG
VSAQDRVTTIKTAANPQAKPEDLARPGHVFPLRARAGGVLARRGHTEGTV
DLMQMAGLQPAGVLCELTNPDGSMAKTPEIIEFGKLHNMPVLTIEDMVQY
RIQFDLKL

Ligand information

• Ligand ID: N52
• InChI: InChI=1S/C5H11O8P/c1-3(6)5(9,4(7)8)2-13-14(10,11)12/h4,7-9H,2H2,1H3,(H2,10,11,12)/t5-/m0/s1
• InChIKey: IYNPDRWOJYWTNN-YFKPBYRVSA-N
• SMILES:
  CACTVS 3.385: CC(=O)[C@@](O)(CO[P](O)(O)=O)C(O)O
  ACDLabs 12.01: O=P(O)(O)OCC(O)(C(O)O)C(C)=O
  OpenEye OEToolkits 2.0.7: CC(=O)C(COP(=O)(O)O)(C(O)O)O
  CACTVS 3.385: CC(=O)[C](O)(CO[P](O)(O)=O)C(O)O
• Formula: C5 H11 O8 P
• Name: (2R)-2-(dihydroxymethyl)-2-hydroxy-3-oxobutyl dihydrogen phosphate
• PDB chain: 7uf5 Chain A Residue 301

Receptor-Ligand Complex Structure

Structure summary

• PDB: 7uf5 Evidence for the Chemical Mechanism of RibB (3,4-Dihydroxy-2-butanone 4-phosphate Synthase) of Riboflavin Biosynthesis.
• Resolution: 2.1 Å
• Binding residue (original residue number in PDB): R38 E39 R151 H154 T155 L173 E175
• Binding residue (residue number reindexed from 1): R37 E38 R142 H145 T146 L164 E166
• Annotation score: 2

Enzymatic activity

• Enzyme Commision number: 4.1.99.12: 3,4-dihydroxy-2-butanone-4-phosphate synthase.

Gene Ontology

Molecular Function

• GO:0000287 magnesium ion binding
• GO:0003824 catalytic activity
• GO:0008686 3,4-dihydroxy-2-butanone-4-phosphate synthase activity
• GO:0016829 lyase activity
• GO:0030145 manganese ion binding
• GO:0046872 metal ion binding

Biological Process

• GO:0009231 riboflavin biosynthetic process

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:7uf5, PDBe:7uf5, PDBj:7uf5
• PDBsum: 7uf5
• PubMed: 35802469
• UniProt: Q9KKP2|RIBB_VIBCH 3,4-dihydroxy-2-butanone 4-phosphate synthase (Gene Name=ribB)