Research workbench

Peptide deformylase (co-form) with mercaptoethanol

Analyse Peptide deformylase (co-form) with mercaptoethanol in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4AL3
Type: protein
Length: 162 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase
EC: 3.5.1.88
UniProt: P0A6K3
Ligands: CO, CL
Pockets: 1 · best druggability 0.46

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide deformylase (EC 3.5.1.88)	protein	162	33% helix, 25% strand	P0A6K3

Ligands and binding sites

CO · Cobalt (II) ion · metal · chains A
CL · Chloride ion · ion · chains A
BME · Beta-mercaptoethanol · 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, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	94	0.46	0.80	20	CL, BME

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

4AL3 · peptide deformylase (Co-form) with mercaptoethanol · the same entry in another collection · chain A against A, TM-score 1.00
P0A6K3 · AlphaFold monomer V2.0 prediction for peptide deformylase (P0A6K3) · a predicted model of the same protein · chain A against A, TM-score 0.99

Analyse

Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
Every structure of UniProt P0A6K3
Elsewhere: RCSB PDB 4AL3 · PDBe 4AL3 · UniProt P0A6K3

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