MolNFT v1 · #92668 · protein + DNA
Topoisomerase II-DNA-amppnp complex
4GFH · DNA topoisomerase 2: “Topoisomerase II-DNA-amppnp complex”. X-ray diffraction, 2 ligands (ANP, MG), 20 pockets (best druggability 0.84). MolNFT v1 #92668 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 4GFH
- Type
- protein + DNA
- Length
- 2,304 residues
- Chains
- 10
- 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
- ANP, MG
- Pockets
- 20 · best druggability 0.84
Structure
x-ray diffraction · 6 distinct chains · 39% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | DNA topoisomerase 2 (EC 5.99.1.3) | protein | 1102 | 39% helix, 20% strand | P06786 |
| B, G | DNA (5'-D(P*CP*CP*TP*AP*CP*TP*GP*CP*TP*AP*C)-3') | dna | 11 | — | — |
| C, H | DNA (5'-D(*CP*GP*CP*GP*GP*TP*AP*GP*CP*AP*GP*TP*AP*GP*G)- 3') | dna | 15 | — | — |
| D, I | DNA (5'-D(P*GP*GP*AP*TP*GP*AP*CP*GP*AP*TP*(TSP))-3') | dna | 11 | — | — |
| E, J | DNA (5'-D(*CP*GP*CP*GP*AP*AP*TP*CP*GP*TP*CP*AP*TP*CP*C)- 3') | dna | 15 | — | — |
| F | DNA topoisomerase 2 (EC 5.99.1.3) | protein | 1098 | 39% helix, 20% strand | P06786 |
Ligands and binding sites
- ANP · Phosphoaminophosphonic acid-adenylate ester · ligand · 2 copies · chains A, F
- MG · Magnesium ion · metal · 2 copies · chains A, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 793 | 0.84 | 0.87 | 73 | empty |
| 2 | 460 | 0.84 | 0.91 | 65 | empty |
| 3 | 448 | 0.83 | 0.91 | 68 | empty |
| 4 | 598 | 0.83 | 0.88 | 62 | empty |
| 5 | 874 | 0.81 | 0.83 | 90 | empty |
Interfaces
41 interfaces between chains.
- A–F · 6739 Ų buried · 91 hydrogen bonds · protein-protein
- H–J · 1764 Ų buried · 587 hydrogen bonds · nucleic-nucleic
- C–E · 1736 Ų buried · 592 hydrogen bonds · nucleic-nucleic
- B–D · 1321 Ų buried · 437 hydrogen bonds · nucleic-nucleic
- G–I · 1301 Ų buried · 430 hydrogen bonds · nucleic-nucleic
Modifications
Observed in the structure: 4 modified (nucleotide modification, 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 4GFH · PDBe 4GFH · UniProt P06786
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