Structure of PDB 3d40 Chain A Binding Site BS01

Receptor Information

>3d40 Chain A (length=252) Species: 43759 (Streptomyces wedmorensis)

SGLVPRGSHMTPDFLAIKVGGSLFSRKDEPGSLDDDAVTRFARNFARLAE
TYRGRMVLISGGGAFAFSLAGLTEATFEVKKRWAEKLRGIGVDAFPLQLA
AMCTLRNGIPQLRSEVLRDVLDHGALPVLAGDALFDEHGKLWAFSSDRVP
EVLLPMVEGRLRVVTLTDVDGIVTDGDTILPEVDARSPEQAYAALWGSSE
GAMHTKLDALVTCARRGAECFIMRGDPGSDLEFLTAPFSSWPAHVRSTRI
TT

Ligand information

• Ligand ID: DPO
• InChI: InChI=1S/H4O7P2/c1-8(2,3)7-9(4,5)6/h(H2,1,2,3)(H2,4,5,6)/p-4
• InChIKey: XPPKVPWEQAFLFU-UHFFFAOYSA-J
• SMILES:
  CACTVS 3.370: [O-][P]([O-])(=O)O[P]([O-])([O-])=O
  OpenEye OEToolkits 1.7.2: [O-]P(=O)([O-])OP(=O)([O-])[O-]
  ACDLabs 12.01: [O-]P([O-])(=O)OP([O-])([O-])=O
• Formula: O7 P2
• Name: DIPHOSPHATE
• PDB chain: 3d40 Chain A Residue 2811

Receptor-Ligand Complex Structure

Structure summary

• PDB: 3d40 Crystal Structure of Fosfomycin Resistance Kinase FomA from Streptomyces wedmorensis.
• Resolution: 1.53 Å
• Binding residue (original residue number in PDB): K9 G11 G12 G52 G53 D150 K216
• Binding residue (residue number reindexed from 1): K18 G20 G21 G61 G62 D147 K206
• Annotation score: 1

Enzymatic activity

• Enzyme Commision number: 2.7.4.26: isopentenyl phosphate kinase.

Gene Ontology

Molecular Function

• GO:0004349 glutamate 5-kinase activity
• GO:0005524 ATP binding
• GO:0016301 kinase activity
• GO:0102043 isopentenyl phosphate kinase activity

Biological Process

• GO:0006561 proline biosynthetic process
• GO:0008299 isoprenoid biosynthetic process
• GO:0016310 phosphorylation

Cellular Component

• GO:0005829 cytosol

External links

• PDB: RCSB:3d40, PDBe:3d40, PDBj:3d40
• PDBsum: 3d40
• PubMed: 18701452
• UniProt: Q56187