Research workbench
Nucleosome core particle with adducts from the anticancer compound, [(ETA6-5,8,9,10-TETRAHYDROANTHRACENE)RU(ETHYLENEDIAMINE)CL][PF6]
Analyse Nucleosome core particle with adducts from the anticancer compound… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5CP6
- Type
- protein + DNA
- Length
- 1,053 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (145-mer); Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1
- UniProt
- P84233, P62799, Q6AZJ8, P02281
- Ligands
- RUH, MG, SO4
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
| A, E | Histone H3.2 | protein | 96 | 67% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 82 | 61% helix, 9% strand | P62799 |
| C, G | Histone H2A | protein | 106 | 58% helix, 7% strand | Q6AZJ8 |
| D, H | Histone H2B 1.1 | protein | 95 | 73% helix, 4% strand | P02281 |
| F | Histone H4 | protein | 87 | 57% helix, 8% strand | P62799 |
Ligands and binding sites
- RUH · (ethane6-5,8,9,10-tetrahydroanthracene)Ru(II)(ethylene-diamine)Cl · ligand · 3 copies · chains I, J
- MG · Magnesium ion · metal · chains E
- SO4 · Sulfate ion · ion · 3 copies · chains J, C, D, I, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 16 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 681 | 0.78 | 0.83 | 63 | empty |
| 2 | 507 | 0.74 | 0.83 | 49 | empty |
| 3 | 308 | 0.73 | 0.86 | 46 | empty |
| 4 | 831 | 0.72 | 0.78 | 88 | empty |
| 5 | 1140 | 0.72 | 0.76 | 85 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6506 Ų buried · 588 hydrogen bonds · nucleic-nucleic
- E–F · 2624 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2609 Ų buried · 25 hydrogen bonds · protein-protein
- C–D · 2584 Ų buried · 23 hydrogen bonds · protein-protein
- A–B · 2566 Ų buried · 26 hydrogen bonds · protein-protein
Compared structures
- 5CP6 · Nucleosome Core Particle with Adducts from the Anticancer Compound… · the same entry in another collection · chain I against I, TM-score 1.00
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 P02281
- Elsewhere: RCSB PDB 5CP6 · PDBe 5CP6 · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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