Research workbench
DNA stretching in the nucleosome facilitates alkylation by an intercalating antitumor agent
Analyse DNA stretching in the nucleosome facilitates alkylation by an intercalating… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3KUY
- Type
- protein + DNA
- Length
- 1,053 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.2; Histone H4; Histone H2A; Histone H2B; DNA (145-mer)
- UniProt
- P84233, P62799, Q6AZJ8, Q92130
- Ligands
- ATV, MN
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 7 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.2 | protein | 96 | 67% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 82 | 60% helix, 9% strand | P62799 |
| C, G | Histone H2A | protein | 106 | 57% helix, 7% strand | Q6AZJ8 |
| D, H | Histone H2B | protein | 95 | 74% helix, 4% strand | Q92130 |
| F | Histone H4 | protein | 87 | 57% helix, 8% strand | P62799 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
Ligands and binding sites
- ATV · 2-[(2R)-oxiran-2-ylmethyl]-1H-benzo[de]isoquinoline-1,3(2H)-dione · ligand · 2 copies · chains I, J
- MN · Manganese (II) ion · metal · chains E, 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 | 775 | 0.80 | 0.83 | 71 | empty |
| 2 | 347 | 0.74 | 0.86 | 47 | empty |
| 3 | 328 | 0.74 | 0.86 | 42 | empty |
| 4 | 834 | 0.72 | 0.77 | 82 | empty |
| 5 | 841 | 0.71 | 0.77 | 64 | ATV |
Interfaces
37 interfaces between chains.
- I–J · 6484 Ų buried · 622 hydrogen bonds · nucleic-nucleic
- E–F · 2671 Ų buried · 23 hydrogen bonds · protein-protein
- C–D · 2658 Ų buried · 27 hydrogen bonds · protein-protein
- G–H · 2623 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2585 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 3KUY · DNA Stretching in the Nucleosome Facilitates Alkylation by an Intercalating Antitumor… · the same entry in another collection · chain J against J, TM-score 1.00
- P84233 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84233) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt Q6AZJ8
- Every structure of UniProt Q92130
- Elsewhere: RCSB PDB 3KUY · PDBe 3KUY · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt Q92130
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