MolNFT v1 · #129542 · protein + DNA
X-ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer
5ONG · DNA (147-mer): “X-ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the…”. X-ray diffraction, 2 ligands (MN, CL), 20 pockets (best druggability 0.80). MolNFT v1 #129542 on GenesisL1…
- PDB
- 5ONG
- Type
- protein + DNA
- Length
- 1,048 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- DNA (147-mer); Histone H3.2; Histone H4; Histone H2A; Histone H2B 1.1
- UniProt
- P84233, P62799, Q6AZJ8, P02281
- Ligands
- MN, CL
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 10 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | DNA (147-mer) | dna | 147 | — | — |
| J | DNA (147-mer) | dna | 147 | — | — |
| A | Histone H3.2 | protein | 96 | 67% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 78 | 63% helix, 9% strand | P62799 |
| C | Histone H2A | protein | 106 | 58% helix, 7% strand | Q6AZJ8 |
| D | Histone H2B 1.1 | protein | 94 | 73% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 97 | 67% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 84 | 60% helix, 8% strand | P62799 |
| G | Histone H2A | protein | 106 | 56% helix, 7% strand | Q6AZJ8 |
| H | Histone H2B 1.1 | protein | 93 | 74% helix, 4% strand | P02281 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 20 copies · chains I, J, E
- CL · Chloride ion · ion · 4 copies · chains A, J, C, D, E, 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, 19 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 776 | 0.80 | 0.84 | 75 | empty |
| 2 | 396 | 0.76 | 0.86 | 44 | empty |
| 3 | 428 | 0.76 | 0.86 | 52 | empty |
| 4 | 787 | 0.70 | 0.76 | 64 | empty |
| 5 | 1074 | 0.69 | 0.74 | 67 | empty |
Interfaces
35 interfaces between chains.
- I–J · 6425 Ų buried · 455 hydrogen bonds · nucleic-nucleic
- C–D · 2659 Ų buried · 24 hydrogen bonds · protein-protein
- G–H · 2612 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2585 Ų buried · 25 hydrogen bonds · protein-protein
- A–B · 2500 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (nucleotide modification).
Compared structures
- 5ONG · X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically… · 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 5ONG · PDBe 5ONG · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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