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Crystal structure of a glycyl radical enzyme from archaeoglobus fulgidus

Analyse Crystal structure of a glycyl radical enzyme from archaeoglobus fulgidus in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 2F3O
Type: protein
Length: 1,546 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Pyruvate formate-lyase 2
UniProt: O28823
Pockets: 17 · best druggability 0.77

Structure

x-ray diffraction · 1 distinct chain · 51% helix, 11% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Pyruvate formate-lyase 2	protein	773	51% helix, 11% strand	O28823

Ligands and binding sites

PGE · Triethylene glycol · additive · 2 copies · chains A, B
GOL · Glycerol · additive · 2 copies · chains A, B

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

Pockets

17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	216	0.77	0.91	43	PGE, GOL
2	83	0.74	0.97	26	empty
3	264	0.74	0.88	52	PGE, GOL
4	761	0.72	0.78	51	empty
5	50	0.69	0.98	18	empty

Interfaces

1 interface between chains.

A–B · 416 Å² buried · 3 hydrogen bonds · protein-protein

Compared structures

2F3O · Crystal Structure of a glycyl radical enzyme from Archaeoglobus fulgidus · 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 O28823
Elsewhere: RCSB PDB 2F3O · PDBe 2F3O · UniProt O28823

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