MolNFT v1 · #97513 · protein + DNA
Nucleosome core particle containing (ETA6-P-cymene)-(1, 2- ethylenediamine)-ruthenium
4KGC · Histone H3.2: “Nucleosome core particle containing (ETA6-P-cymene)-(1, 2- ethylenediamine)-ruthenium”. X-ray diffraction, 3 ligands (HRU, MG, SO4), 20 pockets (best druggability 0.78). MolNFT v1 #97513 on GenesisL1: 3D structure…
- PDB
- 4KGC
- 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
- HRU, 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 |
|---|---|---|---|---|---|
| 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 | 75% 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
- HRU · (ethane-1,2-diamine-kappa~2~N,N')[(1,2,3,4,5,6-eta)-1-methyl-4-(propan-2-yl)cyclohexane-1,2,3,4,5,6-hexayl]ruthenium · ligand · 4 copies · chains C, G, I, J
- 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 673 | 0.78 | 0.83 | 59 | empty |
| 2 | 372 | 0.76 | 0.87 | 47 | empty |
| 3 | 425 | 0.75 | 0.85 | 60 | empty |
| 4 | 931 | 0.74 | 0.78 | 63 | HRU |
| 5 | 761 | 0.72 | 0.78 | 78 | empty |
Interfaces
37 interfaces between chains.
- I–J · 6441 Ų buried · 598 hydrogen bonds · nucleic-nucleic
- E–F · 2610 Ų buried · 22 hydrogen bonds · protein-protein
- C–D · 2600 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 2571 Ų buried · 21 hydrogen bonds · protein-protein
- A–B · 2558 Ų buried · 23 hydrogen bonds · protein-protein
Compared structures
- 4KGC · Nucleosome Core Particle Containing (ETA6-P-CYMENE)-(1, 2-ETHYLENEDIAMINE)-RUTHENIUM · the same entry in another collection · chain H against H, 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 4KGC · PDBe 4KGC · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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