Research workbench
Crystal structure of bacillus subtilis DIMANGANESE(II) nrdf
Analyse Crystal structure of bacillus subtilis DIMANGANESE(II) nrdf in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DR0
- Type
- protein
- Length
- 581 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase subunit beta
- EC
- 1.17.4.1
- UniProt
- P50621
- Ligands
- MN, SO4
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 290 | 77% helix, 0% strand | P50621 |
| B | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 291 | 77% helix, 0% strand | P50621 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 205 | 0.64 | 0.83 | 37 | empty |
| 2 | 357 | 0.60 | 0.77 | 55 | empty |
| 3 | 78 | 0.38 | 0.77 | 16 | empty |
| 4 | 84 | 0.35 | 0.75 | 20 | empty |
| 5 | 58 | 0.30 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1775 Ų buried · 16 hydrogen bonds · protein-protein
Compared structures
- 4DR0 · Crystal structure of Bacillus subtilis dimanganese(II) NrdF · the same entry in another collection · chain A against A, TM-score 1.00
- P50621 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase subunit beta… · a predicted model of the same protein · chain B against A, TM-score 0.99
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 P50621
- Elsewhere: RCSB PDB 4DR0 · PDBe 4DR0 · UniProt P50621
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