Research workbench
X-ray structure of the nucleosome core particle at 2.5 a resolution
Analyse X-ray structure of the nucleosome core particle at 2.5 a resolution in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1EQZ
- Type
- protein + DNA
- Length
- 1,170 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 146 nucleotides long DNA; Protein (histone H2A); Protein (histone H2B); Protein (histone…
- UniProt
- P02263, P02279, P84229, P62801
- Ligands
- MN, K, CL
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 9 distinct chains · 56% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I, J | 146 nucleotides long DNA | dna | 146 | — | — |
| A | Protein (histone H2A) | protein | 125 | 49% helix, 6% strand | P02263 |
| B | Protein (histone H2B) | protein | 108 | 64% helix, 4% strand | P02279 |
| C | Protein (histone H3) | protein | 107 | 60% helix, 4% strand | P84229 |
| D | Protein (histone H4) | protein | 89 | 56% helix, 8% strand | P62801 |
| E | Protein (histone H2A) | protein | 127 | 47% helix, 6% strand | P02263 |
| F | Protein (histone H2B) | protein | 107 | 64% helix, 4% strand | P02279 |
| G | Protein (histone H3) | protein | 120 | 54% helix, 3% strand | P84229 |
| H | Protein (histone H4) | protein | 95 | 53% helix, 7% strand | P62801 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 15 copies · chains I, J
- K · Potassium ion · metal · 7 copies · chains I, J, A, D
- CL · Chloride ion · ion · 2 copies · chains J, A, B, I, E, F
- CAC · Cacodylate ion · additive · chains 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, 20 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 821 | 0.81 | 0.85 | 94 | empty |
| 2 | 830 | 0.80 | 0.83 | 79 | empty |
| 3 | 1102 | 0.76 | 0.79 | 78 | MN, K |
| 4 | 922 | 0.70 | 0.76 | 61 | CL |
| 5 | 758 | 0.70 | 0.77 | 48 | K |
Interfaces
35 interfaces between chains.
- I–J · 6408 Ų buried · 541 hydrogen bonds · nucleic-nucleic
- G–H · 2764 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2654 Ų buried · 30 hydrogen bonds · protein-protein
- C–D · 2597 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2590 Ų buried · 28 hydrogen bonds · protein-protein
Compared structures
- 1EQZ · X-ray structure of the nucleosome core particle at 2.5 a resolution · the same entry in another collection · chain G against G, TM-score 1.00
- P84229 · AlphaFold monomer V2.0 prediction for histone H3.2 (P84229) · a predicted model of the same protein · chain C against A, TM-score 0.91
- P62801 · AlphaFold monomer V2.0 prediction for histone H4 (P62801) · a predicted model of the same protein · chain D against A, TM-score 0.85
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 P02263
- Every structure of UniProt P02279
- Every structure of UniProt P84229
- Every structure of UniProt P62801
- Elsewhere: RCSB PDB 1EQZ · PDBe 1EQZ · UniProt P02263 · UniProt P02279 · UniProt P84229 · UniProt P62801
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