Research workbench
Structure of topoisomerase subunit
Analyse Structure of topoisomerase subunit in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1MX0
- Type
- protein
- Length
- 2,753 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Type II DNA topoisomerase VI subunit B
- EC
- 5.99.1.3
- UniProt
- O05207
- Ligands
- ANP, MG, NA
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 37% helix, 23% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II DNA topoisomerase VI subunit B (EC 5.99.1.3) | protein | 461 | 39% helix, 24% strand | O05207 |
| B | Type II DNA topoisomerase VI subunit B (EC 5.99.1.3) | protein | 455 | 36% helix, 24% strand | O05207 |
| C | Type II DNA topoisomerase VI subunit B (EC 5.99.1.3) | protein | 466 | 38% helix, 24% strand | O05207 |
| D | Type II DNA topoisomerase VI subunit B (EC 5.99.1.3) | protein | 461 | 37% helix, 23% strand | O05207 |
| E | Type II DNA topoisomerase VI subunit B (EC 5.99.1.3) | protein | 456 | 37% helix, 24% strand | O05207 |
| F | Type II DNA topoisomerase VI subunit B (EC 5.99.1.3) | protein | 454 | 34% helix, 22% strand | O05207 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 6 copies · chains A, B, C, D, E, F
- MG · Magnesium ion · metal · 6 copies · chains A, B, C, D, E, F
- NA · Sodium ion · metal · chains D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 209 | 0.84 | 0.97 | 36 | MG, ANP |
| 2 | 236 | 0.82 | 0.94 | 39 | MG, ANP |
| 3 | 229 | 0.81 | 0.94 | 38 | MG, ANP |
| 4 | 229 | 0.81 | 0.94 | 38 | MG, ANP |
| 5 | 264 | 0.81 | 0.93 | 45 | MG, ANP |
Interfaces
6 interfaces between chains.
- C–D · 3472 Ų buried · 57 hydrogen bonds · protein-protein
- A–B · 3426 Ų buried · 59 hydrogen bonds · protein-protein
- E–F · 3321 Ų buried · 52 hydrogen bonds · protein-protein
- C–E · 300 Ų buried · 3 hydrogen bonds · protein-protein
- D–E · 51 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 30 modified (engineered).
Compared structures
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 O05207
- Elsewhere: RCSB PDB 1MX0 · PDBe 1MX0 · UniProt O05207
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