MolNFT v1 · #92218 · protein + DNA
Human topoisomerase iibeta in complex with DNA and ametantrone
4G0W · DNA topoisomerase 2-beta: “Human topoisomerase iibeta in complex with DNA and ametantrone”. X-ray diffraction, 2 ligands (AKE, MG), 16 pockets (best druggability 0.88). MolNFT v1 #92218 on GenesisL1: 3D structure, binding sites and…
- PDB
- 4G0W
- Type
- protein + DNA
- Length
- 1,368 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
- AKE, MG
- Pockets
- 16 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 49% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2-beta (EC 5.99.1.3) | protein | 664 | 49% helix, 14% strand | Q02880 |
| B | DNA topoisomerase 2-beta (EC 5.99.1.3) | protein | 664 | 48% 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
- AKE · 1,4-bis({2-[(2-hydroxyethyl)amino]ethyl}amino)anthracene-9,10-dione · 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
16 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1136 | 0.88 | 0.90 | 150 | MG |
| 2 | 434 | 0.65 | 0.78 | 43 | empty |
| 3 | 433 | 0.63 | 0.77 | 40 | empty |
| 4 | 235 | 0.61 | 0.81 | 28 | AKE |
| 5 | 229 | 0.59 | 0.80 | 24 | MG |
Interfaces
12 interfaces between chains.
- A–B · 1823 Ų buried · 27 hydrogen bonds · protein-protein
- A–F · 986 Ų buried · 21 hydrogen bonds · protein-nucleic
- B–D · 972 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–C · 785 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–E · 772 Ų buried · 11 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 4G0W · PDBe 4G0W · UniProt Q02880
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