Research workbench
Crystal structure of ribonucleotide reductase nrdf from bacillus anthracis soaked with manganese ions
Analyse Crystal structure of ribonucleotide reductase nrdf from bacillus anthracis… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QO9
- Type
- protein
- Length
- 576 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
- Q81TB4
- Ligands
- MN, SO4
- Pockets
- 5 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 78% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 288 | 78% helix, 0% strand | Q81TB4 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 5 copies · chains A, B
- BTB · 2-[bis-(2-hydroxy-ethyl)-amino]-2-hydroxymethyl-propane-1,3-diol · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 196 | 0.53 | 0.78 | 28 | BTB |
| 2 | 124 | 0.44 | 0.77 | 18 | SO4, BTB |
| 3 | 108 | 0.41 | 0.76 | 14 | empty |
| 4 | 57 | 0.33 | 0.77 | 12 | empty |
| 5 | 52 | 0.28 | 0.75 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 2252 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 6QO9 · Crystal structure of ribonucleotide reductase NrdF from Bacillus anthracis soaked with… · 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 Q81TB4
- Elsewhere: RCSB PDB 6QO9 · PDBe 6QO9 · UniProt Q81TB4
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