MolNFT v1 · #32423 · protein
Ribonucleotide reductase class 1B holocomplex R1E,R2F from salmonella typhimurium
2BQ1 · Ribonucleoside-diphosphate reductase 2 alpha subunit: “Ribonucleotide reductase class 1B holocomplex R1E,R2F from salmonella typhimurium”. X-ray diffraction, 3 ligands (DGT, FE, MG), 20 pockets (best druggability 0.74). MolNFT v1…
- PDB
- 2BQ1
- Type
- protein
- Length
- 1,934 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase 2 alpha subunit; Ribonucleoside-diphosphate…
- EC
- 1.17.4.1
- UniProt
- Q08698, P17424
- Ligands
- DGT, FE, MG
- Pockets
- 20 · best druggability 0.74
Structure
x-ray diffraction · 4 distinct chains · 53% helix, 9% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| E | Ribonucleoside-diphosphate reductase 2 alpha subunit (EC 1.17.4.1) | protein | 675 | 47% helix, 13% strand | Q08698 |
| F | Ribonucleoside-diphosphate reductase 2 alpha subunit (EC 1.17.4.1) | protein | 684 | 45% helix, 11% strand | Q08698 |
| I | Ribonucleoside-diphosphate reductase 2 beta subunit (EC 1.17.4.1) | protein | 294 | 71% helix, 0% strand | P17424 |
| J | Ribonucleoside-diphosphate reductase 2 beta subunit (EC 1.17.4.1) | protein | 281 | 67% helix, 0% strand | P17424 |
Ligands and binding sites
- DGT · 2'-deoxyguanosine-5'-triphosphate · ligand · 2 copies · chains E, F
- FE · Fe (III) ion · metal · 4 copies · chains I, J
- MG · Magnesium ion · metal · 2 copies · chains E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 746 | 0.74 | 0.79 | 80 | DGT |
| 2 | 601 | 0.69 | 0.78 | 63 | empty |
| 3 | 509 | 0.63 | 0.76 | 39 | DGT, MG |
| 4 | 101 | 0.52 | 0.83 | 24 | empty |
| 5 | 145 | 0.50 | 0.79 | 35 | empty |
Interfaces
3 interfaces between chains.
- I–J · 1722 Ų buried · 12 hydrogen bonds · protein-protein
- E–F · 1306 Ų buried · 13 hydrogen bonds · protein-protein
- E–I · 1289 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 2BQ1 · Ribonucleotide reductase class 1b holocomplex R1E,R2F from Salmonella typhimurium · the same entry in another collection · chain J against J, TM-score 1.00
- Q08698 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase 2 subunit… · a predicted model of the same protein · chain F against A, TM-score 0.99
- P17424 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase 2 subunit beta… · a predicted model of the same protein · chain J 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 Q08698
- Every structure of UniProt P17424
- Elsewhere: RCSB PDB 2BQ1 · PDBe 2BQ1 · UniProt Q08698 · UniProt P17424
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.