MolNFT v1 · #117843 · protein

R2-like ligand-binding oxidase with aerobically reconstituted MN/FE cofactor (reconstituted in solution)

5EKB · Ribonucleotide reductase small subunit: “R2-like ligand-binding oxidase with aerobically reconstituted MN/FE cofactor (reconstituted in solution)”. X-ray diffraction, 3 ligands (PLM, MN3, FE), 2 pockets (best druggability 0.84).…

PDB: 5EKB
Type: protein
Length: 285 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonucleotide reductase small subunit
EC: 1.17.4.1
UniProt: Q5KW80
Ligands: PLM, MN3, FE
Pockets: 2 · best druggability 0.84

Structure

x-ray diffraction · 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
MN3 · Manganese (III) ion · metal · chains A
FE · Fe (III) ion · metal · 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	226	0.84	0.96	41	PLM
2	59	0.28	0.74	20	empty

Compared structures

5EKB · R2-like ligand-binding oxidase with aerobically reconstituted Mn/Fe cofactor… · 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 5EKB · PDBe 5EKB · UniProt Q5KW80

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