Research workbench
Nucleosome core particle modified with a cisplatin 1,3-cis-{PT(NH3) 2}2+-D(GPTPG) intrastrand cross-link
Analyse Nucleosome core particle modified with a cisplatin 1,3-cis-{PT(NH3)… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O62
- 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 type 1; Histone H2B 1.1; DNA (146-mer)
- UniProt
- P84233, P62799, P06897, P02281
- Ligands
- CPT
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 8 distinct chains · 57% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.2 | protein | 98 | 63% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 80 | 58% helix, 8% strand | P62799 |
| C | Histone H2A type 1 | protein | 105 | 47% helix, 4% strand | P06897 |
| D, H | Histone H2B 1.1 | protein | 95 | 74% helix, 2% strand | P02281 |
| F | Histone H4 | protein | 84 | 55% helix, 7% strand | P62799 |
| G | Histone H2A type 1 | protein | 106 | 46% helix, 4% strand | P06897 |
| I | DNA (146-mer) | dna | 146 | — | — |
| J | DNA (146-mer) | dna | 146 | — | — |
Ligands and binding sites
- CPT · Cisplatin · ligand · chains E, I, J
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 | 817 | 0.80 | 0.83 | 69 | empty |
| 2 | 397 | 0.78 | 0.87 | 45 | empty |
| 3 | 458 | 0.75 | 0.84 | 52 | empty |
| 4 | 937 | 0.72 | 0.77 | 58 | empty |
| 5 | 756 | 0.69 | 0.77 | 57 | CPT |
Interfaces
38 interfaces between chains.
- I–J · 7033 Ų buried · 582 hydrogen bonds · nucleic-nucleic
- G–H · 2709 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2699 Ų buried · 21 hydrogen bonds · protein-protein
- E–F · 2652 Ų buried · 17 hydrogen bonds · protein-protein
- A–B · 2543 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 3O62 · Nucleosome core particle modified with a cisplatin 1,3-cis-{Pt(NH3)2}2+-d(GpTpG)… · 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 0.97
- P06897 · AlphaFold monomer V2.0 prediction for histone H2A type 1 (P06897) · a predicted model of the same protein · chain C 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 P84233
- Every structure of UniProt P62799
- Every structure of UniProt P06897
- Every structure of UniProt P02281
- Elsewhere: RCSB PDB 3O62 · PDBe 3O62 · UniProt P84233 · UniProt P62799 · UniProt P06897 · UniProt P02281
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