MolNFT v1 · #173746 · protein
The serp optimized structure of ribonucleotide reductase from rhodobacter sphaeroides
7B9Q · Vitamin B12-dependent ribonucleotide reductase: “The serp optimized structure of ribonucleotide reductase from rhodobacter sphaeroides”. X-ray diffraction, 2 ligands (DTP, MG), 18 pockets (best druggability 0.78). MolNFT v1 #173746…
- PDB
- 7B9Q
- Type
- protein
- Length
- 1,728 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vitamin B12-dependent ribonucleotide reductase
- EC
- 1.17.4.1
- UniProt
- A0A6H2IRA4
- Ligands
- DTP, MG
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vitamin B12-dependent ribonucleotide reductase (EC 1.17.4.1) | protein | 868 | 43% helix, 14% strand | A0A6H2IRA4 |
| B | Vitamin B12-dependent ribonucleotide reductase (EC 1.17.4.1) | protein | 860 | 38% helix, 10% strand | A0A6H2IRA4 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · 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
18 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 844 | 0.78 | 0.82 | 79 | MG, DTP |
| 2 | 736 | 0.77 | 0.82 | 86 | empty |
| 3 | 470 | 0.68 | 0.79 | 57 | empty |
| 4 | 284 | 0.64 | 0.81 | 41 | empty |
| 5 | 102 | 0.64 | 0.89 | 19 | DTP |
Interfaces
1 interface between chains.
- A–B · 3141 Ų buried · 30 hydrogen bonds · protein-protein
Compared structures
- 7B9Q · The SERp optimized structure of Ribonucleotide reductase from Rhodobacter sphaeroides · 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 A0A6H2IRA4
- Elsewhere: RCSB PDB 7B9Q · PDBe 7B9Q · UniProt A0A6H2IRA4
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.