Research workbench
Structure of full length topoisomerase I from thermotoga maritima in monoclinic crystal form
Analyse Structure of full length topoisomerase I from thermotoga maritima in monoclinic… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2GAJ
- Type
- protein
- Length
- 1,162 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase I
- EC
- 5.99.1.2
- UniProt
- P46799
- Pockets
- 12 · best druggability 0.74
Structure
x-ray diffraction · 1 distinct chain · 40% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase I (EC 5.99.1.2) | protein | 581 | 40% helix, 22% strand | P46799 |
Pockets
12 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 967 | 0.74 | 0.77 | 80 | empty |
| 2 | 851 | 0.73 | 0.78 | 87 | empty |
| 3 | 849 | 0.72 | 0.77 | 63 | empty |
| 4 | 566 | 0.70 | 0.79 | 68 | empty |
| 5 | 261 | 0.55 | 0.77 | 34 | empty |
Interfaces
1 interface between chains.
- A–B · 947 Ų buried · 14 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2GAJ · Structure of Full Length Topoisomerase I from Thermotoga maritima in monoclinic crystal… · the same entry in another collection · chain A against A, TM-score 1.00
- P46799 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 1 (P46799) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P46799
- Elsewhere: RCSB PDB 2GAJ · PDBe 2GAJ · UniProt P46799
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