Research workbench
Human topoisomerase iibeta in complex with DNA and etoposide
Analyse Human topoisomerase iibeta 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
- 3QX3
- Type
- protein + DNA
- Length
- 1,382 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2-beta; DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3'); DNA…
- EC
- 5.99.1.3
- UniProt
- Q02880
- Ligands
- EVP, MG
- Pockets
- 13 · best druggability 0.82
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2-beta (EC 5.99.1.3) | protein | 671 | 49% helix, 15% strand | Q02880 |
| B | DNA topoisomerase 2-beta (EC 5.99.1.3) | protein | 671 | 49% helix, 15% strand | Q02880 |
| 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 A, C, D, F, B, E
- 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
13 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 354 | 0.82 | 0.92 | 59 | MG |
| 2 | 350 | 0.81 | 0.91 | 58 | MG |
| 3 | 637 | 0.81 | 0.87 | 80 | EVP |
| 4 | 440 | 0.64 | 0.78 | 42 | empty |
| 5 | 422 | 0.63 | 0.77 | 42 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1843 Ų buried · 35 hydrogen bonds · protein-protein
- A–F · 968 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–D · 955 Ų buried · 20 hydrogen bonds · protein-nucleic
- B–E · 794 Ų buried · 10 hydrogen bonds · protein-nucleic
- A–C · 791 Ų buried · 12 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 Q02880
- Elsewhere: RCSB PDB 3QX3 · PDBe 3QX3 · UniProt Q02880
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