Research workbench
Human topoisomerase iialpha in complex with DNA and etoposide
Analyse Human topoisomerase iialpha in complex with DNA and etoposide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5GWK
- Type
- protein + DNA
- Length
- 1,488 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2-alpha; DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3'); DNA…
- EC
- 5.99.1.3
- UniProt
- P11388
- Ligands
- EVP, MG
- Pockets
- 18 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 46% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | DNA topoisomerase 2-alpha (EC 5.99.1.3) | protein | 724 | 46% helix, 15% strand | P11388 |
| C, E | DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3') | dna | 8 | — | — |
| D, F | DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3') | dna | 12 | — | — |
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
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, E, D, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 10 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 753 | 0.83 | 0.86 | 99 | MG, EVP |
| 2 | 183 | 0.75 | 0.92 | 34 | MG |
| 3 | 118 | 0.75 | 0.95 | 28 | MG |
| 4 | 327 | 0.75 | 0.87 | 39 | EVP |
| 5 | 424 | 0.72 | 0.83 | 34 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1849 Ų buried · 27 hydrogen bonds · protein-protein
- B–D · 980 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–F · 962 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 803 Ų buried · 14 hydrogen bonds · protein-nucleic
- B–E · 745 Ų buried · 14 hydrogen bonds · protein-nucleic
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 P11388
- Elsewhere: RCSB PDB 5GWK · PDBe 5GWK · UniProt P11388
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