Research workbench
X-ray Structure of the H2A-N38C Nucleosome Core Particle
Analyse X-ray Structure of the H2A-N38C Nucleosome Core Particle in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5OMX
- Type
- protein + DNA
- Length
- 1,052 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.32
- Source
- Homo sapiens; Xenopus laevis
- 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 0.76
Structure
x-ray diffraction · resolution 2.32 · 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 | 97 | 66% helix, 4% strand | P84233 |
| B | Histone H4 | protein | 79 | 62% helix, 8% strand | P62799 |
| C | Histone H2A | protein | 105 | 57% helix, 7% strand | Q6AZJ8 |
| D | Histone H2B 1.1 | protein | 94 | 73% helix, 4% strand | P02281 |
| E | Histone H3.2 | protein | 99 | 67% helix, 4% strand | P84233 |
| F | Histone H4 | protein | 86 | 58% helix, 8% strand | P62799 |
| G | Histone H2A | protein | 103 | 57% helix, 6% strand | Q6AZJ8 |
| H | Histone H2B 1.1 | protein | 95 | 73% helix, 4% strand | P02281 |
Ligands and binding sites
- MN · Manganese (II) ion · metal · 33 copies · chains I, J, E, F
- 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 | 553 | 0.76 | 0.83 | 65 | empty |
| 2 | 416 | 0.76 | 0.86 | 54 | empty |
| 3 | 524 | 0.74 | 0.83 | 57 | empty |
| 4 | 1007 | 0.71 | 0.75 | 70 | empty |
| 5 | 512 | 0.65 | 0.78 | 45 | CL |
Interfaces
36 interfaces between chains.
- I–J · 6486 Ų buried · 488 hydrogen bonds · nucleic-nucleic
- C–D · 2700 Ų buried · 23 hydrogen bonds · protein-protein
- G–H · 2630 Ų buried · 25 hydrogen bonds · protein-protein
- E–F · 2556 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2537 Ų buried · 22 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
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 5OMX · PDBe 5OMX · UniProt P84233 · UniProt P62799 · UniProt Q6AZJ8 · UniProt P02281
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