MolNFT v1 · #88235 · protein
Crystal structure of the anaerobic ribonucleotide reductase from thermotoga maritima with mes in the active site
4COM · Anaerobic ribonucleoside-triphosphate reductase: “Crystal structure of the anaerobic ribonucleotide reductase from thermotoga maritima with mes in the active…”. X-ray diffraction, 1 ligand (ZN), 18 pockets (best druggability 0.85).…
- 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
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