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MolNFT v1 · #123276 · protein

Crystal structure of type 2 pdf from streptococcus agalactiae in complex with actinonin

5JF1 · Peptide deformylase: “Crystal structure of type 2 pdf from streptococcus agalactiae in complex with actinonin”. X-ray diffraction, 2 ligands (BB2, ZN), 1 pocket (best druggability 0.51). MolNFT v1 #123276 on GenesisL1: 3D structure…

PDB
5JF1
Type
protein
Length
203 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Peptide deformylase
EC
3.5.1.88
UniProt
Q8E378
Ligands
BB2, ZN
Pockets
1 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 30% helix, 24% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APeptide deformylase (EC 3.5.1.88)protein20330% helix, 24% strandQ8E378

Ligands and binding sites

  • BB2 · Actinonin · ligand · chains A
  • ZN · Zinc ion · metal · 8 copies · chains A
  • ACT · Acetate ion · 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
11250.510.8119BB2, ZN

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

  • 5JF1 · Crystal structure of type 2 PDF from Streptococcus agalactiae in complex with actinonin · the same entry in another collection · chain A against A, TM-score 1.00
  • Q8E378 · AlphaFold monomer V2.0 prediction for peptide deformylase (Q8E378) · a predicted model of the same protein · chain A against A, TM-score 0.99

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