Research workbench
Human topoisomerase iibeta in complex with DNA
Analyse Human topoisomerase iibeta in complex with DNA in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4J3N
- Type
- protein + DNA
- Length
- 1,375 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
- MG
- Pockets
- 15 · best druggability 0.88
Structure
x-ray diffraction · 5 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 | 666 | 49% helix, 15% strand | Q02880 |
| B | DNA topoisomerase 2-beta (EC 5.99.1.3) | protein | 670 | 49% helix, 15% strand | Q02880 |
| C, E | DNA (5'-D(P*AP*GP*CP*CP*GP*AP*GP*C)-3') | dna | 8 | — | — |
| D | DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3') | dna | 12 | — | — |
| F | DNA (5'-D(P*TP*GP*CP*AP*GP*CP*TP*CP*GP*GP*CP*T)-3') | dna | 11 | — | — |
Ligands and binding sites
- MG · Magnesium ion · metal · 7 copies · chains A, C, F, B, E, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
15 pockets found on a 1 Å grid, 9 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 877 | 0.88 | 0.90 | 112 | MG |
| 2 | 350 | 0.82 | 0.92 | 56 | MG |
| 3 | 445 | 0.67 | 0.79 | 47 | empty |
| 4 | 561 | 0.66 | 0.77 | 54 | empty |
| 5 | 389 | 0.62 | 0.78 | 42 | empty |
Interfaces
10 interfaces between chains.
- A–B · 1799 Ų buried · 30 hydrogen bonds · protein-protein
- B–D · 1077 Ų buried · 25 hydrogen bonds · protein-nucleic
- A–F · 1016 Ų buried · 19 hydrogen bonds · protein-nucleic
- A–C · 839 Ų buried · 11 hydrogen bonds · protein-nucleic
- B–E · 838 Ų buried · 9 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 4J3N · PDBe 4J3N · UniProt Q02880
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