MolNFT v2 · #129970 · protein + DNA
X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the histone octamer and the two H2A/H2B dimers crosslinked via H2A N38C
5ONW: “X-Ray crystal structure of a nucleosome core particle with its DNA site-specifically crosslinked to the…”. X-ray diffraction at 2.8, 2 ligands (MN, CL). MolNFT v2 #129970 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5ONW
- Type
- protein + DNA
- Length
- 1,045 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.8
- Source
- Homo sapiens; Xenopus laevis
- UniProt
- P84233, P62799, Q6AZJ8, P02281
- Ligands
- MN, CL
Structure
x-ray diffraction · resolution 2.8 · 10 distinct chains.
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | — | dna | 147 | — | — |
| J | — | dna | 147 | — | — |
| A | — | protein | 96 | — | P84233 |
| B | — | protein | 78 | — | P62799 |
| C | — | protein | 103 | — | Q6AZJ8 |
| D | — | protein | 96 | — | P02281 |
| E | — | protein | 95 | — | P84233 |
| F | — | protein | 86 | — | P62799 |
| G | — | protein | 105 | — | Q6AZJ8 |
| H | — | protein | 92 | — | P02281 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 20 copies · chains I, J, D, E
- CL · Chloride ion · ion · 4 copies · chains A, C, D, E, G, H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Compared structures
- 5ONW · X-ray crystal structure of a nucleosome core particle with its DNA site-specifically… · 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 E against A, TM-score 0.98
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 5ONW · PDBe 5ONW · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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