MolNFT v1 · #172299 · protein + DNA
Cryo-EM structure of the human topoisomerase II alpha DNA- BINDING/CLEAVAGE domain in state 2
6ZY6 · DNA topoisomerase 2-alpha: “Cryo-EM structure of the human topoisomerase II alpha DNA- BINDING/CLEAVAGE domain in state 2”. Electron microscopy, 1 ligand (EVP), 20 pockets (best druggability 0.86). MolNFT v1 #172299 on GenesisL1: 3D…
- PDB
- 6ZY6
- Type
- protein + DNA
- Length
- 1,580 residues
- Chains
- 6
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2-alpha; DNA (5'- D(*CP*GP*CP*GP*CP*AP*TP*CP*GP*TP*CP*AP*TP*CP*CP*TP*C)…
- EC
- 5.6.2.2
- UniProt
- P11388
- Ligands
- EVP
- Pockets
- 20 · best druggability 0.86
Structure
electron microscopy · 3 distinct chains · 43% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase 2-alpha (EC 5.6.2.2) | protein | 760 | 43% helix, 12% strand | P11388 |
| D, F | DNA (5'- D(*CP*GP*CP*GP*CP*AP*TP*CP*GP*TP*CP*AP*TP*CP*CP*TP*C)-3') | dna | 17 | — | — |
| E, C | DNA (5'-D(*GP*AP*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*G)-3') | dna | 13 | — | — |
Ligands and binding sites
- EVP · (5s,5ar,8ar,9r)-9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5A,6,8,8A,9-hexahydrofuro[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl 4,6-O-[(1R)-ethylidene]-beta-D-glucopyranoside · ligand · 2 copies · chains B, D, E, F, A, C
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 | 983 | 0.86 | 0.87 | 91 | empty |
| 2 | 1199 | 0.85 | 0.86 | 82 | empty |
| 3 | 775 | 0.83 | 0.86 | 75 | EVP |
| 4 | 320 | 0.79 | 0.89 | 56 | empty |
| 5 | 659 | 0.79 | 0.84 | 57 | EVP |
Interfaces
10 interfaces between chains.
- A–B · 2031 Ų buried · 10 hydrogen bonds · protein-protein
- B–F · 889 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 864 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–E · 807 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 799 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 6ZY6 · Cryo-EM structure of the Human topoisomerase II alpha DNA-binding/cleavage domain in… · the same entry in another collection · chain D against D, TM-score 1.00
- P11388 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 2-alpha (P11388) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 P11388
- Elsewhere: RCSB PDB 6ZY6 · PDBe 6ZY6 · UniProt P11388
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