MolNFT v1 · #120962 · protein

Crystal structure of a peptide deformylase from burkholderia ambifaria

5HGW: “Crystal structure of a peptide deformylase from burkholderia ambifaria”. X-ray diffraction, 2 ligands (FE, SO4), 2 pockets (best druggability 0.38). MolNFT v1 #120962 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5HGW
Type: protein
Length: 348 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Peptide deformylase
EC: 3.5.1.88
UniProt: B1YSH1
Ligands: FE, SO4
Pockets: 2 · best druggability 0.38

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 32% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Peptide deformylase (EC 3.5.1.88)	protein	174	26% helix, 32% strand	B1YSH1

Ligands and binding sites

FE · Fe (III) ion · metal · 2 copies · chains A, B
SO4 · Sulfate ion · ion · 8 copies · chains A, B
EDO · 1,2-ethanediol · additive · 4 copies · chains A, B

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	91	0.38	0.76	22	empty
2	79	0.35	0.75	16	EDO

Interfaces

1 interface between chains.

A–B · 822 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

5HGW · Crystal structure of a peptide deformylase from Burkholderia ambifaria · the same entry in another collection · chain A against A, TM-score 1.00

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 B1YSH1
Elsewhere: RCSB PDB 5HGW · PDBe 5HGW · UniProt B1YSH1

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