Research workbench

S.AUREUS polypeptide deformylase

Analyse S.AUREUS polypeptide deformylase in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2AI9
Type: protein
Length: 366 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase
EC: 3.5.1.88
UniProt: P68826
Ligands: NI, SO4
Pockets: 3 · best druggability 0.56

Structure

x-ray diffraction · 1 distinct chain · 29% helix, 25% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Peptide deformylase (EC 3.5.1.88)	protein	183	29% helix, 25% strand	P68826

Ligands and binding sites

NI · Nickel (II) ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 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	151	0.56	0.82	19	empty
2	152	0.52	0.80	18	empty
3	51	0.30	0.76	13	empty

Interfaces

1 interface between chains.

A–B · 409 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

2AI9 · S.aureus Polypeptide Deformylase · the same entry in another collection · chain A against A, TM-score 1.00
P68826 · AlphaFold monomer V2.0 prediction for peptide deformylase (P68826) · a predicted model of the same protein · chain B against A, TM-score 0.98

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 P68826
Elsewhere: RCSB PDB 2AI9 · PDBe 2AI9 · UniProt P68826

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