Research workbench

E.coli deformylase with Co(II) and hydrosulfide

Analyse E.coli deformylase with Co(II) and hydrosulfide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4AZ4
Type: protein
Length: 163 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.8
Source: ESCHERICHIA COLI
Molecule: Peptide deformylase
EC: 3.5.1.88
UniProt: P0A6K3
Ligands: CO, H2S
Pockets: 1 · best druggability 0.45

Structure

x-ray diffraction · resolution 1.8 · 1 distinct chain · 34% helix, 26% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide deformylase (EC 3.5.1.88)	protein	163	34% helix, 26% strand	P0A6K3

Ligands and binding sites

CO · Cobalt (II) ion · metal · chains A
H2S · Hydrosulfuric acid · ion · 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	120	0.45	0.78	21	CO, H2S

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

4AZ4 · E.COLI deformylase with CO(II) and hydrosulfide · 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 4AZ4 · PDBe 4AZ4 · UniProt P0A6K3

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