Research workbench
Crystal structure of the topoisomerase VI holoenzyme from methanosarcina mazei
Analyse Crystal structure of the topoisomerase VI holoenzyme from methanosarcina mazei in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2Q2E
- Type
- protein
- Length
- 896 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II DNA topoisomerase VI subunit a; Type 2 DNA topoisomerase 6 subunit B
- EC
- 5.99.1.3
- UniProt
- Q8PUB7, Q8PUB8
- Pockets
- 16 · best druggability 0.78
Structure
x-ray diffraction · 2 distinct chains · 28% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II DNA topoisomerase VI subunit a (EC 5.99.1.3) | protein | 315 | 33% helix, 6% strand | Q8PUB7 |
| B | Type 2 DNA topoisomerase 6 subunit B (EC 5.99.1.3) | protein | 581 | 25% helix, 18% strand | Q8PUB8 |
Pockets
16 pockets found on a 1 Å grid, 12 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 733 | 0.78 | 0.82 | 89 | empty |
| 2 | 122 | 0.76 | 0.95 | 21 | empty |
| 3 | 157 | 0.74 | 0.91 | 27 | empty |
| 4 | 280 | 0.73 | 0.86 | 42 | empty |
| 5 | 121 | 0.71 | 0.91 | 25 | empty |
Interfaces
1 interface between chains.
- A–B · 1007 Ų buried · 10 hydrogen bonds · protein-protein
Compared structures
- 2Q2E · Crystal structure of the topoisomerase VI holoenzyme from Methanosarcina mazei · the same entry in another collection · chain A against A, TM-score 1.00
- Q8PUB7 · AlphaFold monomer V2.0 prediction for type 2 DNA topoisomerase 6 subunit a (Q8PUB7) · a predicted model of the same protein · chain A against A, TM-score 0.96
- Q8PUB8 · AlphaFold monomer V2.0 prediction for type 2 DNA topoisomerase 6 subunit B (Q8PUB8) · a predicted model of the same protein · chain B against A, TM-score 0.79
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 Q8PUB7
- Every structure of UniProt Q8PUB8
- Elsewhere: RCSB PDB 2Q2E · PDBe 2Q2E · UniProt Q8PUB7 · UniProt Q8PUB8
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