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K3U bound crystal peptide deformylase from acinetobacter baumanii

Analyse K3U bound crystal peptide deformylase from acinetobacter baumanii in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6JEW
Type: protein
Length: 338 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase
EC: 3.5.1.88
UniProt: A0A0J1A8B1
Ligands: K3U, ZN
Pockets: 3 · best druggability 0.75

Structure

x-ray diffraction · 1 distinct chain · 38% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Peptide deformylase (EC 3.5.1.88)	protein	169	38% helix, 27% strand	A0A0J1A8B1

Ligands and binding sites

K3U · S-(2-oxo-2-phenylethyl) (2R)-2-benzyl-4,4,4-trifluorobutanethioate · ligand · chains B
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

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	898	0.75	0.78	84	K3U
2	216	0.56	0.79	33	empty
3	63	0.27	0.73	11	empty

Interfaces

1 interface between chains.

A–B · 404 Å² buried · 7 hydrogen bonds · protein-protein

Compared structures

6JEW · K3U bound crystal peptide deformylase from Acinetobacter baumanii · 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 A0A0J1A8B1
Elsewhere: RCSB PDB 6JEW · PDBe 6JEW · UniProt A0A0J1A8B1

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