MolNFT v1 · #172301 · protein + DNA
Cryo-EM structure of the entire human topoisomerase II alpha in state 2
6ZY8 · DNA topoisomerase 2-alpha: “Cryo-EM structure of the entire human topoisomerase II alpha in state 2”. Electron microscopy, 2 ligands (ANP, EVP), 20 pockets (best druggability 0.87). MolNFT v1 #172301 on GenesisL1: 3D structure…
- PDB
- 6ZY8
- Type
- protein + DNA
- Length
- 2,378 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
- ANP, EVP
- Pockets
- 20 · best druggability 0.87
Structure
electron microscopy · 3 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase 2-alpha (EC 5.6.2.2) | protein | 1159 | 39% helix, 17% 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
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, B
- 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 | 818 | 0.87 | 0.89 | 83 | empty |
| 2 | 886 | 0.86 | 0.87 | 97 | EVP |
| 3 | 1117 | 0.84 | 0.85 | 78 | empty |
| 4 | 262 | 0.81 | 0.92 | 52 | empty |
| 5 | 345 | 0.81 | 0.91 | 45 | ANP |
Interfaces
10 interfaces between chains.
- A–B · 4821 Ų buried · 43 hydrogen bonds · protein-protein
- B–F · 890 Ų buried · 11 hydrogen bonds · protein-nucleic
- A–D · 865 Ų buried · 3 hydrogen bonds · protein-nucleic
- B–E · 806 Ų buried · 13 hydrogen bonds · protein-nucleic
- A–C · 800 Ų buried · 14 hydrogen bonds · protein-nucleic
Compared structures
- 6ZY8 · Cryo-EM structure of the entire Human topoisomerase II alpha in State 2 · 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 0.64
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 6ZY8 · PDBe 6ZY8 · UniProt P11388
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