Research workbench
X-ray crystal structure of bacillus subtilis ribonucleotide reductase nrde alpha subunit with ttp and ADP
Analyse X-ray crystal structure of bacillus subtilis ribonucleotide reductase nrde… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6MV9
- Type
- protein
- Length
- 1,352 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase
- EC
- 1.17.4.1
- UniProt
- A0A162Q3J9
- Ligands
- TTP, ADP, MG
- Pockets
- 20 · best druggability 0.68
Structure
x-ray diffraction · 2 distinct chains · 46% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 674 | 46% helix, 11% strand | A0A162Q3J9 |
| B | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 678 | 46% helix, 12% strand | A0A162Q3J9 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, B
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.68 | 0.76 | 87 | empty |
| 2 | 171 | 0.66 | 0.87 | 28 | empty |
| 3 | 353 | 0.63 | 0.79 | 40 | empty |
| 4 | 177 | 0.62 | 0.84 | 27 | TTP |
| 5 | 61 | 0.55 | 0.88 | 17 | empty |
Interfaces
1 interface between chains.
- A–B · 1512 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide (disulfide).
Compared structures
- 6MV9 · X-ray crystal structure of Bacillus subtilis ribonucleotide reductase NrdE alpha subunit… · 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 A0A162Q3J9
- Elsewhere: RCSB PDB 6MV9 · PDBe 6MV9 · UniProt A0A162Q3J9
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.