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Crystal structure of maize PDRP bound with AMP and Hg2+

Analyse Crystal structure of maize PDRP bound with AMP and Hg2+ in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
5D1F
Type
protein
Length
274 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v2 / PDB Bank
Contract
0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner
0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution
3.4
Source
Zea mays
Molecule
Pyruvate, phosphate dikinase regulatory protein, chloroplastic
EC
2.7.11.32, 2.7.4.27
UniProt
Q195N6
Ligands
AMP, HG, MG
Pockets
1 · best druggability 0.39

Structure

x-ray diffraction · resolution 3.4 · 1 distinct chain · 47% helix, 14% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APyruvate, phosphate dikinase regulatory protein, chloroplastic (EC 2.7.11.32, 2.7.4.27)protein27447% helix, 14% strandQ195N6

Ligands and binding sites

  • AMP · Adenosine monophosphate · ligand · chains A
  • HG · Mercury (II) ion · metal · chains A
  • MG · Magnesium ion · metal · 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, 0 with a druggability of 0.5 or more.

PocketVolume (ų)DruggabilityBuriednessLining residuesInside
11330.390.7425AMP, MG

Modifications

Observed in the structure: 1 disulfide (disulfide).

Compared structures

  • 5D1F · Crystal structure of maize pdrp bound with AMP and HG2+ · the same entry in another collection · chain A against A, TM-score 1.00
  • Q195N6 · AlphaFold monomer V2.0 prediction for pyruvate, phosphate dikinase regulatory protein… · a predicted model of the same protein · chain A against A, TM-score 0.98

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