Research workbench
Topoisomerase VI-B, ADP pi bound dimer form
Analyse Topoisomerase VI-B, ADP pi bound dimer form in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1Z5C
- Type
- protein
- Length
- 926 residues
- Chains
- 2
- 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
- ADP, MG, PO4
- Pockets
- 9 · best druggability 0.82
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 24% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Type II DNA topoisomerase VI subunit B (EC 5.99.1.3) | protein | 466 | 38% helix, 24% strand | O05207 |
| B | Type II DNA topoisomerase VI subunit B (EC 5.99.1.3) | protein | 460 | 37% helix, 24% strand | O05207 |
Ligands and binding sites
- ADP · Adenosine-5'-diphosphate · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 2 copies · chains A, B
- PO4 · Phosphate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 224 | 0.82 | 0.95 | 36 | MG, PO4, ADP |
| 2 | 222 | 0.82 | 0.95 | 36 | MG, PO4, ADP |
| 3 | 1035 | 0.82 | 0.83 | 132 | empty |
| 4 | 727 | 0.76 | 0.81 | 78 | empty |
| 5 | 64 | 0.55 | 0.87 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 3502 Ų buried · 48 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 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 1Z5C · PDBe 1Z5C · UniProt O05207
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