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MolNFT v1 · #116034 · protein

Crystal structure of maize pdrp bound with AMP and HG2+

5D1F · Pyruvate, phosphate dikinase regulatory protein…: “Crystal structure of maize pdrp bound with AMP and HG2+”. X-ray diffraction, 3 ligands (AMP, HG, MG), 1 pocket (best druggability 0.39). MolNFT v1 #116034 on GenesisL1: 3D…

PDB
5D1F
Type
protein
Length
274 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
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 · 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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