Research workbench
Topoisomerase II-DNA cleavage complex, metal-bound
Analyse Topoisomerase II-DNA cleavage complex, metal-bound in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3L4K
- Type
- protein + DNA
- Length
- 772 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA topoisomerase 2; DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3'); DNA…
- EC
- 5.99.1.3
- UniProt
- P06786
- Ligands
- TSP, ZN
- Pockets
- 9 · best druggability 0.84
Structure
x-ray diffraction · 5 distinct chains · 43% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2 (EC 5.99.1.3) | protein | 721 | 43% helix, 16% strand | P06786 |
| B | DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3') | dna | 11 | — | — |
| C | DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)- 3') | dna | 15 | — | — |
| D | DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*)-3') | dna | 10 | — | — |
| E | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)- 3') | dna | 15 | — | — |
Ligands and binding sites
- TSP · 3'-thio-thymidine-5'-phosphate · ligand · chains A, B, C, D, E
- ZN · Zinc ion · metal · 8 copies · chains A, B, C, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 980 | 0.84 | 0.86 | 93 | empty |
| 2 | 832 | 0.77 | 0.81 | 79 | ZN |
| 3 | 255 | 0.61 | 0.81 | 34 | empty |
| 4 | 132 | 0.41 | 0.75 | 20 | empty |
| 5 | 153 | 0.40 | 0.73 | 28 | ZN |
Interfaces
10 interfaces between chains.
- C–E · 1765 Ų buried · 591 hydrogen bonds · nucleic-nucleic
- B–D · 1200 Ų buried · 401 hydrogen bonds · nucleic-nucleic
- A–C · 1026 Ų buried · 16 hydrogen bonds · protein-nucleic
- A–E · 1007 Ų buried · 20 hydrogen bonds · protein-nucleic
- A–B · 717 Ų buried · 15 hydrogen bonds · protein-nucleic
Modifications
Observed in the structure: 3 covalent, 1 modified (covalent ligand, phosphorylation).
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 P06786
- Elsewhere: RCSB PDB 3L4K · PDBe 3L4K · UniProt P06786
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