MolNFT v1 · #107218 · protein
Anaerobic ribonucleotide reductase
4U3E · Ribonucleoside triphosphate reductase: “Anaerobic ribonucleotide reductase”. X-ray diffraction, 2 ligands (ZN, NA), 14 pockets (best druggability 0.89). MolNFT v1 #107218 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4U3E
- Type
- protein
- Length
- 1,256 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside triphosphate reductase
- EC
- 1.17.4.2
- UniProt
- Q9WYL6
- Ligands
- ZN, NA
- Pockets
- 14 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside triphosphate reductase (EC 1.17.4.2) | protein | 637 | 51% helix, 15% strand | Q9WYL6 |
| B | Ribonucleoside triphosphate reductase (EC 1.17.4.2) | protein | 619 | 50% helix, 16% strand | Q9WYL6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- NA · Sodium ion · metal · chains A
- CIT · Citric acid · additive · 2 copies · chains A, B
- GOL · Glycerol · additive · 2 copies · chains A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 953 | 0.89 | 0.91 | 104 | CIT, NA, ACT |
| 2 | 134 | 0.69 | 0.89 | 22 | CIT |
| 3 | 113 | 0.66 | 0.89 | 25 | empty |
| 4 | 76 | 0.62 | 0.90 | 20 | empty |
| 5 | 269 | 0.58 | 0.78 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 4523 Ų buried · 54 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 40 modified (engineered).
Compared structures
- 4U3E · Anaerobic ribonucleotide reductase · 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 Q9WYL6
- Elsewhere: RCSB PDB 4U3E · PDBe 4U3E · UniProt Q9WYL6
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