MolNFT v1 · #31058 · protein

E.COLI polypeptide deformylase complexed with sb-485343

2AI8: “E.COLI polypeptide deformylase complexed with sb-485343”. X-ray diffraction, 2 ligands (SB7, NI), 5 pockets (best druggability 0.66). MolNFT v1 #31058 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2AI8
Type: protein
Length: 496 residues
Chains: 3
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase
EC: 3.5.1.88
UniProt: P0A6K3
Ligands: SB7, NI
Pockets: 5 · best druggability 0.66

Structure

x-ray diffraction · 2 distinct chains · 36% helix, 27% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Peptide deformylase (EC 3.5.1.88)	protein	166	36% helix, 25% strand	P0A6K3
B	Peptide deformylase (EC 3.5.1.88)	protein	164	35% helix, 29% strand	P0A6K3

Ligands and binding sites

SB7 · [hydroxy(3-phenylpropyl)amino]methanol · ligand · 3 copies · chains A, B, C
NI · Nickel (II) ion · metal · 3 copies · chains A, B, C

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

Pockets

5 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	539	0.66	0.77	70	NI, SB7
2	163	0.52	0.79	24	SB7
3	126	0.40	0.75	24	empty
4	56	0.28	0.74	13	empty
5	50	0.27	0.75	12	empty

Interfaces

2 interfaces between chains.

A–C · 610 Å² buried · 10 hydrogen bonds · protein-protein
B–C · 270 Å² buried · 5 hydrogen bonds · protein-protein

Compared structures

2AI8 · E.coli Polypeptide Deformylase complexed with SB-485343 · 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 C 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 P0A6K3
Elsewhere: RCSB PDB 2AI8 · PDBe 2AI8 · UniProt P0A6K3

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