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Crystal structure of arabidopsis thaliana peptide deformylase 1B (ATPDF1B) G41Q mutant in complex with actinonin

Analyse Crystal structure of arabidopsis thaliana peptide deformylase 1B (ATPDF1B) G41Q… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB
3M6Q
Type
protein
Length
181 residues
Chains
1
Method
x-ray diffraction
Collection
MolNFT v1 / PDB
Contract
0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner
0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule
Peptide deformylase 1B
EC
3.5.1.88
UniProt
Q9FUZ2
Ligands
BB2, ZN
Pockets
1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 25% strand (DSSP).

ChainMoleculeTypeResiduesSecondary structureUniProt
APeptide deformylase 1B (EC 3.5.1.88)protein18136% helix, 25% strandQ9FUZ2

Ligands and binding sites

  • BB2 · Actinonin · ligand · chains A
  • ZN · Zinc ion · metal · 5 copies · 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
1960.460.8019BB2

Compared structures

  • 3M6Q · Crystal structure of Arabidopsis thaliana peptide deformylase 1B (AtPDF1B) G41Q mutant in… · the same entry in another collection · chain A against A, TM-score 1.00
  • Q9FUZ2 · AlphaFold monomer V2.0 prediction for peptide deformylase 1B, CHLOROPLASTIC/MITOCHONDRIAL… · a predicted model of the same protein · chain A against A, TM-score 0.99

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