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Phosphotransferase related to CoA biosynthesis pathway

Analyse Phosphotransferase related to CoA biosynthesis pathway in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
6JBC
Type
protein
Length
295 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
2.7
Source
Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
Molecule
Pantoate kinase
EC
2.7.1.169
UniProt
Q5JHF1
Ligands
PPV, CA, NA
Pockets
1 · best druggability 0.61

Structure

x-ray diffraction · resolution 2.7 · 1 distinct chain · 36% helix, 31% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APantoate kinase (EC 2.7.1.169)protein29536% helix, 31% strandQ5JHF1

Ligands and binding sites

  • PPV · Pyrophosphate · ligand · chains A
  • CA · Calcium ion · metal · 3 copies · chains A
  • NA · Sodium ion · metal · 2 copies · chains A
  • GOL · Glycerol · additive · 3 copies · chains A
  • PG4 · Tetraethylene glycol · additive · chains A
  • EDO · 1,2-ethanediol · additive · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
13510.610.7751GOL, PPV

Compared structures

  • 6JBC · Phosphotransferase related to CoA biosynthesis pathway · the same entry in another collection · chain A against A, TM-score 1.00
  • Q5JHF1 · AlphaFold monomer V2.0 prediction for pantoate kinase (Q5JHF1) · a predicted model of the same protein · chain A against A, TM-score 0.98

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