Research workbench
Crystal structure of bacillus cereus ribonucleotide reductase di-iron nrdf in complex with nrdi (1.8 a resolution)
Analyse Crystal structure of bacillus cereus ribonucleotide reductase di-iron nrdf in… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4BMO
- Type
- protein
- Length
- 408 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, B0YPL1
- Ligands
- FMN, FE2, CL
- Pockets
- 4 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 68% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 290 | 78% helix, 0% strand | Q81G55 |
| B | Nrdi | protein | 118 | 42% helix, 24% strand | B0YPL1 |
Ligands and binding sites
- FMN · Flavin mononucleotide · ligand · chains A, B
- FE2 · Fe (II) ion · metal · 2 copies · chains A
- CL · Chloride ion · ion · 5 copies · 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, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 214 | 0.81 | 0.94 | 33 | CL, FMN |
| 2 | 110 | 0.59 | 0.86 | 21 | empty |
| 3 | 104 | 0.40 | 0.76 | 16 | empty |
| 4 | 57 | 0.39 | 0.81 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 977 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 4BMO · 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 B0YPL1
- Elsewhere: RCSB PDB 4BMO · PDBe 4BMO · UniProt Q81G55 · UniProt B0YPL1
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