MolNFT v1 · #120321 · protein + DNA
Structure of a human topoisomerase iibeta fragment in complex with DNA and E7873R
5GWI · DNA topoisomerase 2-beta: “Structure of a human topoisomerase iibeta fragment in complex with DNA and E7873R”. X-ray diffraction, 3 ligands (N2R, N2N, MG), 18 pockets (best druggability 0.88). MolNFT v1 #120321 on GenesisL1: 3D…
- PDB
- 5GWI
- 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
- N2R, N2N, MG
- Pockets
- 18 · best druggability 0.88
Structure
x-ray diffraction · 4 distinct chains · 48% helix, 14% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2-beta (EC 5.99.1.3) | protein | 671 | 48% helix, 14% strand | Q02880 |
| B | DNA topoisomerase 2-beta (EC 5.99.1.3) | protein | 671 | 48% helix, 14% 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
- N2R · dichloro{4,5-di(amino-kappaN)-N-[9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydro-2H-furo[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl]pentanamide}platinum · ligand · 2 copies · chains A, C, D, F, B, E
- N2N · dichloro{4,5-di(amino-kappaN)-N-[9-(4-hydroxy-3,5-dimethoxyphenyl)-8-oxo-5,5a,6,8,8a,9-hexahydro-2H-furo[3',4':6,7]naphtho[2,3-d][1,3]dioxol-5-yl]pentanamide}platinum · ligand · 2 copies · chains A, C, D, F, B, E
- MG · Magnesium ion · metal · 6 copies · chains A, C, B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
18 pockets found on a 1 Å grid, 11 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 835 | 0.88 | 0.90 | 119 | MG |
| 2 | 315 | 0.71 | 0.85 | 25 | empty |
| 3 | 382 | 0.68 | 0.81 | 30 | empty |
| 4 | 212 | 0.66 | 0.85 | 24 | N2R, N2N |
| 5 | 175 | 0.66 | 0.86 | 26 | N2R, N2N |
Interfaces
10 interfaces between chains.
- A–B · 1826 Ų buried · 31 hydrogen bonds · protein-protein
- A–F · 942 Ų buried · 18 hydrogen bonds · protein-nucleic
- B–D · 937 Ų buried · 17 hydrogen bonds · protein-nucleic
- A–C · 813 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–E · 799 Ų buried · 12 hydrogen bonds · protein-nucleic
Compared structures
- 5GWI · Structure of a Human topoisomerase IIbeta fragment in complex with DNA and E7873R · the same entry in another collection · chain F against F, TM-score 1.00
- Q02880 · AlphaFold monomer V2.0 prediction for DNA topoisomerase 2-beta (Q02880) · a predicted model of the same protein · chain A 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 Q02880
- Elsewhere: RCSB PDB 5GWI · PDBe 5GWI · UniProt Q02880
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