Research workbench
Crystal structure of the anaerobic ribonucleotide reductase from thermotoga maritima with mes in the active site
Analyse Crystal structure of the anaerobic ribonucleotide reductase from thermotoga… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4COM
- Type
- protein
- Length
- 1,197 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
- ZN
- Pockets
- 18 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Anaerobic ribonucleoside-triphosphate reductase (EC 1.17.4.2) | protein | 601 | 50% helix, 15% strand | Q9WYL6 |
| B | Anaerobic ribonucleoside-triphosphate reductase (EC 1.17.4.2) | protein | 596 | 49% helix, 15% strand | Q9WYL6 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B
- MES · 2-(N-morpholino)-ethanesulfonic acid · additive · 2 copies · chains A, B
- 1PE · Pentaethylene glycol · additive · 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 489 | 0.85 | 0.91 | 53 | 1PE |
| 2 | 199 | 0.76 | 0.91 | 40 | MES |
| 3 | 122 | 0.67 | 0.90 | 24 | empty |
| 4 | 98 | 0.64 | 0.89 | 17 | MES |
| 5 | 94 | 0.62 | 0.89 | 21 | empty |
Interfaces
1 interface between chains.
- A–B · 3990 Ų buried · 45 hydrogen bonds · protein-protein
Compared structures
- 4COM · 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 4COM · PDBe 4COM · UniProt Q9WYL6
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.