Research workbench
Cryo-EM structure of the human topoisomerase II alpha DNA- BINDING/CLEAVAGE domain in state 1
Analyse Cryo-EM structure of the human topoisomerase II alpha DNA- BINDING/CLEAVAGE… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6ZY5
- 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 0.85
Structure
electron microscopy · 3 distinct chains · 44% helix, 10% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B, A | DNA topoisomerase 2-alpha (EC 5.6.2.2) | protein | 760 | 44% helix, 10% 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, F, C, A, E
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 | 585 | 0.85 | 0.91 | 68 | empty |
| 2 | 348 | 0.83 | 0.93 | 62 | empty |
| 3 | 992 | 0.76 | 0.79 | 79 | empty |
| 4 | 184 | 0.76 | 0.92 | 40 | EVP |
| 5 | 587 | 0.75 | 0.82 | 51 | empty |
Interfaces
12 interfaces between chains.
- B–A · 3805 Ų buried · 28 hydrogen bonds · protein-protein
- D–A · 875 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–F · 865 Ų buried · 12 hydrogen bonds · protein-nucleic
- C–A · 715 Ų buried · 8 hydrogen bonds · protein-nucleic
- B–E · 706 Ų buried · 10 hydrogen bonds · protein-nucleic
Compared structures
- 6ZY5 · Cryo-EM structure of the Human topoisomerase II alpha DNA-binding/cleavage domain in… · the same entry in another collection · chain E against E, TM-score 1.00
- P11388 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 2-alpha (P11388) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 6ZY5 · PDBe 6ZY5 · UniProt P11388
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