Research workbench
Crystal structure of ribonucleotide reductase nrdf L61G variant from bacillus anthracis anaerobically soaked with FE(II) and MN(II) ions
Analyse Crystal structure of ribonucleotide reductase nrdf L61G variant from bacillus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6TQY
- Type
- protein
- Length
- 573 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
- 6 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 79% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase subunit beta (EC 1.17.4.1) | protein | 285 | 79% helix, 0% strand | Q81TB4 |
| 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
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 63 | 0.74 | 0.98 | 18 | empty |
| 2 | 244 | 0.52 | 0.75 | 30 | empty |
| 3 | 156 | 0.47 | 0.77 | 20 | SO4 |
| 4 | 52 | 0.38 | 0.81 | 17 | empty |
| 5 | 63 | 0.32 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 2372 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 6TQY · Crystal structure of ribonucleotide reductase NrdF L61G variant from Bacillus anthracis… · 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 6TQY · PDBe 6TQY · UniProt Q81TB4
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