MolNFT v1 · #139417 · protein + DNA
Nucleosome core particle with an adduct of a binuclear rapta (ru- arene-phosphaadamantane) compound having a 1,2- diphenylethylenediamine linker (R,R-configuration)
5XF3 · Histone H3.1: “Nucleosome core particle with an adduct of a binuclear rapta (ru- arene-phosphaadamantane) compound having a…”. X-ray diffraction, 4 ligands (RUD, RRK, MG), 20 pockets (best druggability 0.76). MolNFT v1 #139417 on…
- PDB
- 5XF3
- Type
- protein + DNA
- Length
- 1,056 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A type 1-B/E; Histone H2B type 1-J; DNA (145-mer)
- UniProt
- P68431, P62805, P04908, P06899
- Ligands
- RUD, RRK, MG, SO4
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 8 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 98 | 65% helix, 4% strand | P68431 |
| B | Histone H4 | protein | 82 | 61% helix, 7% strand | P62805 |
| C, G | Histone H2A type 1-B/E | protein | 106 | 56% helix, 7% strand | P04908 |
| D, H | Histone H2B type 1-J | protein | 95 | 73% helix, 4% strand | P06899 |
| E | Histone H3.1 | protein | 97 | 68% helix, 4% strand | P68431 |
| F | Histone H4 | protein | 87 | 57% helix, 8% strand | P62805 |
| 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
- RRK · (1R,2R)-1,2-diphenylethane-1,2-diamine · ligand · chains G, H
- MG · Magnesium ion · metal · chains E, F
- SO4 · Sulfate ion · ion · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 560 | 0.76 | 0.83 | 52 | empty |
| 2 | 368 | 0.76 | 0.86 | 49 | empty |
| 3 | 381 | 0.75 | 0.86 | 45 | empty |
| 4 | 356 | 0.71 | 0.83 | 48 | empty |
| 5 | 700 | 0.67 | 0.76 | 49 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6454 Ų buried · 582 hydrogen bonds · nucleic-nucleic
- E–F · 2637 Ų buried · 26 hydrogen bonds · protein-protein
- C–D · 2598 Ų buried · 20 hydrogen bonds · protein-protein
- G–H · 2590 Ų buried · 22 hydrogen bonds · protein-protein
- A–B · 2523 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 5XF3 · 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 P68431
- Every structure of UniProt P62805
- Every structure of UniProt P04908
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 5XF3 · PDBe 5XF3 · UniProt P68431 · UniProt P62805 · UniProt P04908 · UniProt P06899
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.