Research workbench

Peptide deformylase catalytic core (residues 1-147), NMR, 9 structures

Analyse Peptide deformylase catalytic core (residues 1-147), NMR, 9 structures in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 1DEF
Type: protein
Length: 147 residues
Chains: 1
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase
EC: 3.5.1.31
UniProt: P0A6K3
Ligands: ZN
Pockets: 3 · best druggability 0.45

Structure

solution nmr · 1 distinct chain · 18% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide deformylase (EC 3.5.1.31)	protein	147	18% helix, 17% strand	P0A6K3

Ligands and binding sites

ZN · Zinc ion · metal · chains A

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

Pockets

3 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	95	0.45	0.80	19	empty
2	79	0.41	0.79	26	empty
3	55	0.34	0.78	16	empty

Compared structures

1DEF · Peptide deformylase catalytic core (residues 1-147), NMR, 9 structures · the same entry in another collection · chain A against A, TM-score 1.00
P0A6K3 · AlphaFold monomer V2.0 prediction for peptide deformylase (P0A6K3) · a predicted model of the same protein · chain A against A, TM-score 0.58

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 P0A6K3
Elsewhere: RCSB PDB 1DEF · PDBe 1DEF · UniProt P0A6K3

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.