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MolNFT v1 · #65381 · protein

Crystal structure of calcineurin-like phosphoesterase yfkn from bacillus subtilis

3GVE · Yfkn protein: “Crystal structure of calcineurin-like phosphoesterase yfkn from bacillus subtilis”. X-ray diffraction, 2 ligands (MG, MN), 1 pocket (best druggability 0.76). MolNFT v1 #65381 on GenesisL1: 3D structure, binding sites…

PDB
3GVE
Type
protein
Length
668 residues
Chains
2
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Yfkn protein
UniProt
O34313
Ligands
MG, MN
Pockets
1 · best druggability 0.76

Structure

x-ray diffraction · 1 distinct chain · 31% helix, 28% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
A, BYfkn proteinprotein33431% helix, 28% strandO34313

Ligands and binding sites

  • MG · Magnesium ion · metal · 3 copies · chains A, B
  • MN · Manganese (II) ion · metal · 2 copies · chains A, B
  • CIT · Citric acid · additive · 2 copies · chains A, B

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
111730.760.78109empty

Interfaces

1 interface between chains.

  • A–B · 677 Ų buried · 11 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 12 modified (engineered).

Compared structures

  • 3GVE · Crystal structure of calcineurin-like phosphoesterase YfkN from Bacillus subtilis · the same entry in another collection · chain B against B, TM-score 1.00
  • O34313 · AlphaFold monomer V2.0 prediction for trifunctional nucleotide phosphoesterase protein… · a predicted model of the same protein · chain A against A, TM-score 0.99

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