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Structure of M. tuberculosis cysq, a pap phosphatase with AMP, PO4, and 2MG bound

Analyse Structure of M. tuberculosis cysq, a pap phosphatase with AMP, PO4, and 2MG… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5DJI
Type
protein
Length
252 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
3'-phosphoadenosine 5'-phosphate phosphatase
EC
3.1.3.7, 3.1.3.11, 3.1.3.25
UniProt
P9WKJ0
Ligands
AMP, MG, PO4
Pockets
1 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 23% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A3'-phosphoadenosine 5'-phosphate phosphatase (EC 3.1.3.7, 3.1.3.11, 3.1.3.25)protein25238% helix, 23% strandP9WKJ0

Ligands and binding sites

  • AMP · Adenosine monophosphate · ligand · chains A
  • MG · Magnesium ion · metal · 2 copies · chains A
  • PO4 · Phosphate ion · ion · 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
11800.550.8026AMP, PO4

Compared structures

  • 5DJI · Structure of M. tuberculosis CysQ, a PAP phosphatase with AMP, PO4, and 2Mg bound · the same entry in another collection · chain A against A, TM-score 1.00
  • P9WKJ0 · AlphaFold monomer V2.0 prediction for 3'-phosphoadenosine 5'-phosphate phosphatase… · a predicted model of the same protein · chain A against A, TM-score 0.97

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