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R2-like ligand-binding oxidase with aerobically reconstituted metal cofactor before photoconversion

Analyse R2-like ligand-binding oxidase with aerobically reconstituted metal cofactor… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5OMK
Type: protein
Length: 285 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v2 / PDB Bank
Contract: 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
Owner: 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
Resolution: 1.704
Source: Geobacillus kaustophilus (strain HTA426)
Molecule: Ribonucleotide reductase small subunit
EC: 1.17.4.1
UniProt: Q5KW80
Ligands: PLM, FE
Pockets: 2 · best druggability 0.82

Structure

x-ray diffraction · resolution 1.704 · 1 distinct chain · 79% helix, 0% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonucleotide reductase small subunit (EC 1.17.4.1)	protein	285	79% helix, 0% strand	Q5KW80

Ligands and binding sites

PLM · Palmitic acid · ligand · chains A
FE · Fe (III) ion · metal · 2 copies · 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	258	0.82	0.93	44	PLM
2	57	0.28	0.74	17	empty

Compared structures

5OMK · R2-like ligand-binding oxidase with aerobically reconstituted metal cofactor before… · 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 Q5KW80
Elsewhere: RCSB PDB 5OMK · PDBe 5OMK · UniProt Q5KW80

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