MolNFT v1 · #172866 · protein
Ribonucleotide reductase R1 protein from aquifex aeolicus
7AGJ · Ribonucleoside-diphosphate reductase subunit alpha: “Ribonucleotide reductase R1 protein from aquifex aeolicus”. X-ray diffraction, 3 ligands (ATP, MG, SO4), 12 pockets (best druggability 0.76). MolNFT v1 #172866 on GenesisL1: 3D…
- PDB
- 7AGJ
- Type
- protein
- Length
- 1,452 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase subunit alpha
- EC
- 1.17.4.1
- UniProt
- O66503
- Ligands
- ATP, MG, SO4
- Pockets
- 12 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 48% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase subunit alpha (EC 1.17.4.1) | protein | 731 | 48% helix, 12% strand | O66503 |
| B | Ribonucleoside-diphosphate reductase subunit alpha (EC 1.17.4.1) | protein | 721 | 49% helix, 12% strand | O66503 |
Ligands and binding sites
- ATP · Adenosine-5'-triphosphate · ligand · 4 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 11 copies · chains A, B
- PEG · Di(hydroxyethyl)ether · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 293 | 0.76 | 0.88 | 40 | empty |
| 2 | 630 | 0.70 | 0.78 | 79 | PEG |
| 3 | 689 | 0.70 | 0.78 | 79 | GOL, SO4 |
| 4 | 445 | 0.69 | 0.80 | 41 | ATP, MG, SO4 |
| 5 | 484 | 0.68 | 0.79 | 42 | ATP, MG |
Interfaces
1 interface between chains.
- A–B · 1766 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 disulfide (disulfide).
Compared structures
- 7AGJ · Ribonucleotide Reductase R1 protein from Aquifex aeolicus · the same entry in another collection · chain A against A, TM-score 1.00
- O66503 · AlphaFold monomer V2.0 prediction for ribonucleoside-diphosphate reductase subunit alpha… · 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 O66503
- Elsewhere: RCSB PDB 7AGJ · PDBe 7AGJ · UniProt O66503
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