MolNFT v1 · #123272 · protein

Crystal structure of type 2 pdf from streptococcus agalactiae, crystallized in imidazole buffer

5JEX · Peptide deformylase: “Crystal structure of type 2 pdf from streptococcus agalactiae, crystallized in imidazole buffer”. X-ray diffraction, 1 ligand (ZN), 1 pocket (best druggability 0.57). MolNFT v1 #123272 on GenesisL1: 3D…

PDB: 5JEX
Type: protein
Length: 203 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase
EC: 3.5.1.88
UniProt: Q8E378
Ligands: ZN
Pockets: 1 · best druggability 0.57

Structure

x-ray diffraction · 1 distinct chain · 28% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide deformylase (EC 3.5.1.88)	protein	203	28% helix, 24% strand	Q8E378

Ligands and binding sites

ZN · Zinc ion · metal · 9 copies · chains A
IMD · Imidazole · additive · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	131	0.57	0.83	22	empty

Modifications

Observed in the structure: 1 modified (oxidation).

Compared structures

5JEX · Crystal structure of type 2 PDF from Streptococcus agalactiae, crystallized in imidazole… · the same entry in another collection · chain A against A, TM-score 1.00
Q8E378 · AlphaFold monomer V2.0 prediction for peptide deformylase (Q8E378) · 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 Q8E378
Elsewhere: RCSB PDB 5JEX · PDBe 5JEX · UniProt Q8E378

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