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Solution structure of peptide deformylase complexed with actinonin

Analyse Solution structure of peptide deformylase complexed with actinonin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2KMN
Type: protein
Length: 147 residues
Chains: 1
Method: solution nmr
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase
EC: 3.5.1.88
UniProt: P0A6K3
Ligands: BB2, ZN
Pockets: 2 · best druggability 0.47

Structure

solution nmr · 1 distinct chain · 26% helix, 35% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide deformylase (EC 3.5.1.88)	protein	147	26% helix, 35% strand	P0A6K3

Ligands and binding sites

BB2 · Actinonin · ligand · chains A
ZN · Zinc ion · metal · chains A

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

Pockets

2 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	116	0.47	0.79	24	BB2
2	53	0.32	0.77	17	empty

Compared structures

2KMN · Solution structure of peptide deformylase complexed with actinonin · 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 0.91

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 2KMN · PDBe 2KMN · UniProt P0A6K3

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