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The crystal structure of the peptide deformylase from vibrio cholerae O1 biovar el tor str. N16961

Analyse The crystal structure of the peptide deformylase from vibrio cholerae O1 biovar… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3FWX
Type: protein
Length: 330 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase
UniProt: A5F4B3
Ligands: ZN
Pockets: 4 · best druggability 0.49

Structure

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

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Peptide deformylase	protein	165	35% helix, 27% strand	A5F4B3

Ligands and binding sites

ZN · Zinc ion · metal · 2 copies · chains A, B

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

Pockets

4 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	111	0.49	0.81	22	empty
2	111	0.48	0.80	19	empty
3	113	0.34	0.73	13	empty
4	63	0.31	0.75	12	empty

Interfaces

1 interface between chains.

A–B · 117 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 modified (engineered).

Compared structures

3FWX · The crystal structure of the peptide deformylase from Vibrio cholerae O1 biovar El Tor… · 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 A5F4B3
Elsewhere: RCSB PDB 3FWX · PDBe 3FWX · UniProt A5F4B3

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