MolNFT v1 · #139420 · protein + DNA
Nucleosome core particle with an adduct of a binuclear rapta (ru- arene-phosphaadamantane) compound having an ethylenediamine linker
5XF6 · Histone H3.2: “Nucleosome core particle with an adduct of a binuclear rapta (ru- arene-phosphaadamantane) compound having an…”. X-ray diffraction, 4 ligands (RUD, EDN, MG), 20 pockets (best druggability 0.81). MolNFT v1 #139420 on…
- PDB
- 5XF6
- Type
- protein + DNA
- Length
- 1,055 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 1.1; DNA (145-mer)
- UniProt
- P84233, P62799, Q6AZJ8, P02281
- Ligands
- RUD, EDN, MG, SO4
- Pockets
- 20 · best druggability 0.81
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 | 97 | 65% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 82 | 61% helix, 9% strand | P62799 |
| C, G | Histone H2A | protein | 106 | 57% 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 |
| I | DNA (145-mer) | dna | 145 | — | — |
| J | DNA (145-mer) | dna | 145 | — | — |
Ligands and binding sites
- RUD · [ethane6-3-(p-tolyl)propanoic acid]Ru(1,3,5-triaza-7-phosphaadamantane)Cl2 · ligand · 2 copies · chains G, H
- EDN · Ethane-1,2-diamine · ligand
- MG · Magnesium ion · metal · chains E
- SO4 · Sulfate ion · ion · 3 copies · chains C, D, J, G, H, I
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1122 | 0.81 | 0.83 | 113 | empty |
| 2 | 465 | 0.74 | 0.83 | 49 | empty |
| 3 | 866 | 0.73 | 0.78 | 89 | empty |
| 4 | 293 | 0.72 | 0.86 | 37 | empty |
| 5 | 628 | 0.71 | 0.79 | 51 | empty |
Interfaces
37 interfaces between chains.
- I–J · 6403 Ų buried · 545 hydrogen bonds · nucleic-nucleic
- C–D · 2639 Ų buried · 24 hydrogen bonds · protein-protein
- E–F · 2628 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 2604 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2565 Ų buried · 27 hydrogen bonds · protein-protein
Compared structures
- 5XF6 · Nucleosome core particle with an adduct of a binuclear RAPTA (Ru-arene-phosphaadamantane)… · the same entry in another collection · chain A against A, 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 5XF6 · PDBe 5XF6 · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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