Research workbench
Thermotoga maritima ribonucleotide reductase, nrdj, in complex with dttp and adenosylcobalamin
Analyse Thermotoga maritima ribonucleotide reductase, nrdj, in complex with dttp and… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O0N
- Type
- protein
- Length
- 1,218 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ribonucleoside-diphosphate reductase
- EC
- 1.17.4.1
- UniProt
- O33839
- Ligands
- TTP, B12, 5AD, MG, CO, CL
- Pockets
- 8 · best druggability 0.70
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 607 | 47% helix, 14% strand | O33839 |
| B | Ribonucleoside-diphosphate reductase (EC 1.17.4.1) | protein | 611 | 48% helix, 15% strand | O33839 |
Ligands and binding sites
- TTP · Thymidine-5'-triphosphate · ligand · 2 copies · chains A, B
- B12 · Cobalamin · ligand · chains B
- 5AD · 5'-deoxyadenosine · ligand · chains B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- CO · Cobalt (II) ion · metal
- CL · Chloride ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 567 | 0.70 | 0.79 | 78 | 5AD |
| 2 | 657 | 0.70 | 0.78 | 69 | TTP |
| 3 | 574 | 0.67 | 0.77 | 59 | empty |
| 4 | 471 | 0.65 | 0.78 | 66 | empty |
| 5 | 125 | 0.56 | 0.83 | 21 | TTP |
Interfaces
1 interface between chains.
- A–B · 1180 Ų buried · 9 hydrogen bonds · protein-protein
Compared structures
- 3O0N · Thermotoga maritima Ribonucleotide Reductase, NrdJ, in complex with dTTP and… · the same entry in another collection · chain B against B, 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 O33839
- Elsewhere: RCSB PDB 3O0N · PDBe 3O0N · UniProt O33839
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