MolNFT v1 · #153452 · protein

K4U bound crystal peptide deformylase from acinetobacter baumanii

6JEX: “K4U bound crystal peptide deformylase from acinetobacter baumanii”. X-ray diffraction, 2 ligands (LHY, ZN), 3 pockets (best druggability 0.74). MolNFT v1 #153452 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 6JEX
Type: protein
Length: 344 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: LHY, ZN
Pockets: 3 · best druggability 0.74

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	172	38% helix, 27% strand	A0A0J1A8B1

Ligands and binding sites

LHY · L-[(N-hydroxyamino)carbonyl]phenylalanine · 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	886	0.74	0.78	79	LHY
2	115	0.53	0.82	21	empty
3	77	0.30	0.73	17	empty

Interfaces

1 interface between chains.

A–B · 372 Å² buried · 6 hydrogen bonds · protein-protein

Compared structures

6JEX · K4U 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 6JEX · PDBe 6JEX · UniProt A0A0J1A8B1

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