MolNFT v1 · #86969 · protein

Crystal structure of bacillus cereus ribonucleotide reductase di-iron nrdf in complex with nrdi (2.1 a resolution)

4BMP · Ribonucleoside-diphosphate reductase subunit beta: “Crystal structure of bacillus cereus ribonucleotide reductase di-iron nrdf in complex with nrdi (2.1 a…”. X-ray diffraction, 3 ligands (FMN, FE2, CL), 4 pockets (best druggability…

PDB: 4BMP
Type: protein
Length: 407 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Ribonucleoside-diphosphate reductase subunit beta; Nrdi
EC: 1.17.4.1
UniProt: Q81G55, Q81G57
Ligands: FMN, FE2, CL
Pockets: 4 · best druggability 0.83

Structure

x-ray diffraction · 2 distinct chains · 66% helix, 7% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1)	protein	290	76% helix, 0% strand	Q81G55
B	Nrdi	protein	117	40% helix, 24% strand	Q81G57

Ligands and binding sites

FMN · Flavin mononucleotide · ligand · chains A, B
FE2 · Fe (II) ion · metal · 2 copies · chains A
CL · Chloride ion · ion · chains A, B

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

Pockets

4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	240	0.83	0.95	42	CL, FMN
2	145	0.65	0.87	24	empty
3	174	0.54	0.79	28	empty
4	97	0.39	0.76	15	empty

Interfaces

1 interface between chains.

A–B · 965 Å² buried · 9 hydrogen bonds · protein-protein

Compared structures

4BMP · Crystal Structure of Bacillus cereus Ribonucleotide Reductase di- iron NrdF in Complex… · 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 Q81G55
Every structure of UniProt Q81G57
Elsewhere: RCSB PDB 4BMP · PDBe 4BMP · UniProt Q81G55 · UniProt Q81G57

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