MolNFT v1 · #88234 · protein
Crystal structure of the anaerobic ribonucleotide reductase from thermotoga maritima with datp bound in the specificity site
4COL · Anaerobic ribonucleoside-triphosphate reductase: “Crystal structure of the anaerobic ribonucleotide reductase from thermotoga maritima with datp bound in the…”. X-ray diffraction, 4 ligands (DTP, SFO, ZN), 12 pockets (best…
- PDB
- 4COL
- Type
- protein
- Length
- 1,179 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anaerobic ribonucleoside-triphosphate reductase
- EC
- 1.17.4.2
- UniProt
- Q9WYL6
- Ligands
- DTP, SFO, ZN, MG
- Pockets
- 12 · best druggability 0.87
Structure
x-ray diffraction · 2 distinct chains · 51% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anaerobic ribonucleoside-triphosphate reductase (EC 1.17.4.2) | protein | 586 | 51% helix, 16% strand | Q9WYL6 |
| B | Anaerobic ribonucleoside-triphosphate reductase (EC 1.17.4.2) | protein | 593 | 52% helix, 16% strand | Q9WYL6 |
Ligands and binding sites
- DTP · 2'-deoxyadenosine 5'-triphosphate · ligand · 2 copies · chains A, B
- SFO · Sulfonic acid · ligand · 2 copies · chains A, B
- ZN · Zinc ion · metal · 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
12 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 936 | 0.87 | 0.88 | 106 | SFO |
| 2 | 77 | 0.62 | 0.90 | 20 | empty |
| 3 | 235 | 0.62 | 0.81 | 29 | MG, DTP |
| 4 | 240 | 0.60 | 0.80 | 25 | MG, DTP |
| 5 | 225 | 0.57 | 0.79 | 39 | empty |
Interfaces
1 interface between chains.
- A–B · 3627 Ų buried · 37 hydrogen bonds · protein-protein
Compared structures
- 4COL · Crystal structure of the anaerobic ribonucleotide reductase from Thermotoga maritima with… · 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 4COL · PDBe 4COL · UniProt Q9WYL6
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