MolNFT v1 · #71758 · protein + DNA
A ruthenium antitumour agent forms specific histone protein adducts in the nucleosome core
3MNN · Histone H3.2: “A ruthenium antitumour agent forms specific histone protein adducts in the nucleosome core”. X-ray diffraction, 5 ligands (MML, PTW, RU), 20 pockets (best druggability 0.80). MolNFT v1 #71758 on GenesisL1: 3D…
- PDB
- 3MNN
- 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
- MML, PTW, RU, MG, SO4
- 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 | 97 | 65% 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 | 74% 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
- MML · 1-methyl-4-(1-methylethyl)benzene · ligand · 3 copies · chains E, F, G, H
- PTW · 1,3,5-triaza-7-phosphatricyclo[3.3.1.1~3,7~]decane · ligand · 3 copies · chains F, G, H
- RU · Ruthenium ion · metal · 3 copies · chains F, G, H
- MG · Magnesium ion · metal · chains E, F
- 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 | 782 | 0.80 | 0.83 | 84 | empty |
| 2 | 316 | 0.73 | 0.86 | 47 | empty |
| 3 | 971 | 0.73 | 0.77 | 63 | empty |
| 4 | 298 | 0.72 | 0.86 | 39 | empty |
| 5 | 665 | 0.72 | 0.79 | 52 | empty |
Interfaces
37 interfaces between chains.
- I–J · 6423 Ų buried · 603 hydrogen bonds · nucleic-nucleic
- C–D · 2645 Ų buried · 23 hydrogen bonds · protein-protein
- E–F · 2627 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 2624 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2568 Ų buried · 24 hydrogen bonds · protein-protein
Compared structures
- 3MNN · A Ruthenium Antitumour Agent Forms Specific Histone Protein Adducts in the Nucleosome Core · 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 P02281
- Elsewhere: RCSB PDB 3MNN · PDBe 3MNN · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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