MolNFT v1 · #56322 · protein
Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms
2ZBK · Type II DNA topoisomerase VI subunit a: “Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer mechanisms”. X-ray diffraction, 1 ligand (RDC), 20 pockets (best druggability 0.77). MolNFT v1 #56322 on…
- PDB
- 2ZBK
- Type
- protein
- Length
- 3,412 residues
- Chains
- 8
- 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
- O05208, O05207
- Ligands
- RDC
- Pockets
- 20 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 37% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, E, G | Type II DNA topoisomerase VI subunit a (EC 5.99.1.3) | protein | 347 | 40% helix, 12% strand | O05208 |
| B, D, F, H | Type 2 DNA topoisomerase 6 subunit B (EC 5.99.1.3) | protein | 506 | 35% helix, 20% strand | O05207 |
Ligands and binding sites
- RDC · Radicicol · ligand · 4 copies · chains B, D, F, H
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 | 185 | 0.77 | 0.92 | 26 | empty |
| 2 | 184 | 0.75 | 0.91 | 27 | empty |
| 3 | 178 | 0.75 | 0.91 | 27 | empty |
| 4 | 968 | 0.74 | 0.77 | 89 | RDC |
| 5 | 176 | 0.73 | 0.90 | 25 | empty |
Interfaces
7 interfaces between chains.
- E–G · 2367 Ų buried · 59 hydrogen bonds · protein-protein
- A–C · 2362 Ų buried · 61 hydrogen bonds · protein-protein
- G–H · 1353 Ų buried · 8 hydrogen bonds · protein-protein
- A–B · 1333 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 1323 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2ZBK · Crystal structure of an intact type II DNA topoisomerase: insights into DNA transfer… · the same entry in another collection · chain H against H, TM-score 1.00
- O05208 · AlphaFold monomer V2.0 prediction for type 2 DNA topoisomerase 6 subunit a (O05208) · a predicted model of the same protein · chain A against A, TM-score 0.94
- O05207 · AlphaFold monomer V2.0 prediction for type 2 DNA topoisomerase 6 subunit B (O05207) · a predicted model of the same protein · chain B against A, TM-score 0.87
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 O05208
- Every structure of UniProt O05207
- Elsewhere: RCSB PDB 2ZBK · PDBe 2ZBK · UniProt O05208 · UniProt O05207
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