MolNFT v1 · #52537 · protein

Formate complex of the ni-form of E.COLI deformylase

2W3U · Peptide deformylase: “Formate complex of the ni-form of E.COLI deformylase”. X-ray diffraction, 1 ligand (NI), 2 pockets (best druggability 0.51). MolNFT v1 #52537 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 2W3U
Type: protein
Length: 165 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase
EC: 3.5.1.31
UniProt: P0A6K3
Ligands: NI
Pockets: 2 · best druggability 0.51

Structure

x-ray diffraction · 1 distinct chain · 36% helix, 24% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Peptide deformylase (EC 3.5.1.31)	protein	165	36% helix, 24% strand	P0A6K3

Ligands and binding sites

NI · Nickel (II) ion · metal · chains A
FMT · Formic acid · additive · 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, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	138	0.51	0.80	25	NI, FMT
2	55	0.29	0.75	14	empty

Compared structures

2W3U · formate complex of the Ni-Form of E.coli deformylase · 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 0.99

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 2W3U · PDBe 2W3U · UniProt P0A6K3

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