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Structure of helicobacter pylori peptide deformylase in complex with inhibitor

Analyse Structure of helicobacter pylori peptide deformylase in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2EW6
Type: protein
Length: 166 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase
EC: 3.5.1.88
UniProt: Q672W7
Ligands: Y13, CO
Pockets: 2 · best druggability 0.49

Structure

x-ray diffraction · 1 distinct chain · 35% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide deformylase (EC 3.5.1.88)	protein	166	35% helix, 27% strand	Q672W7

Ligands and binding sites

Y13 · (2E)-3-(3,4-dihydroxyphenyl)-N-[2-(4-hydroxyphenyl)ethyl]acrylamide · ligand · chains A
CO · Cobalt (II) ion · metal · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Pockets

2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	122	0.49	0.80	18	Y13
2	51	0.29	0.75	11	empty

Compared structures

2EW6 · Structure of Helicobacter Pylori peptide deformylase in complex with inhibitor · the same entry in another collection · chain A against A, TM-score 1.00

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 Q672W7
Elsewhere: RCSB PDB 2EW6 · PDBe 2EW6 · UniProt Q672W7

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