Research workbench
Crystal structure of the nucleosome core particle containing the histone domain of MACROH2A
Analyse Crystal structure of the nucleosome core particle containing the histone domain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1U35
- Type
- protein + DNA
- Length
- 1,049 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Alpha-satellite DNA; Histone H3.1; HIST1H4I protein; H2A histone family; Histone 3, H2BA
- UniProt
- P68433, Q5T006, O75367, Q9D2U9
- Pockets
- 20 · best druggability 0.78
Structure
x-ray diffraction · 8 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| I | Alpha-satellite DNA | dna | 145 | — | — |
| J | Alpha-satellite DNA | dna | 145 | — | — |
| A, E | Histone H3.1 | protein | 98 | 63% helix, 4% strand | P68433 |
| B | HIST1H4I protein | protein | 79 | 58% helix, 9% strand | Q5T006 |
| C, G | H2A histone family | protein | 106 | 58% helix, 7% strand | O75367 |
| D | Histone 3, H2BA | protein | 93 | 73% helix, 4% strand | Q9D2U9 |
| F | HIST1H4I protein | protein | 83 | 60% helix, 8% strand | Q5T006 |
| H | Histone 3, H2BA | protein | 96 | 70% helix, 4% strand | Q9D2U9 |
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 | 608 | 0.78 | 0.83 | 62 | empty |
| 2 | 601 | 0.76 | 0.82 | 54 | empty |
| 3 | 627 | 0.75 | 0.82 | 49 | empty |
| 4 | 129 | 0.70 | 0.91 | 23 | empty |
| 5 | 623 | 0.67 | 0.77 | 62 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6312 Ų buried · 541 hydrogen bonds · nucleic-nucleic
- G–H · 2656 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 2643 Ų buried · 20 hydrogen bonds · protein-protein
- E–F · 2619 Ų buried · 28 hydrogen bonds · protein-protein
- A–B · 2476 Ų buried · 25 hydrogen bonds · protein-protein
Compared structures
- 1U35 · Crystal structure of the nucleosome core particle containing the histone domain of… · the same entry in another collection · chain H against H, TM-score 1.00
- P68433 · AlphaFold monomer V2.0 prediction for histone H3.1 (P68433) · a predicted model of the same protein · chain A against A, TM-score 0.98
- O75367 · AlphaFold monomer V2.0 prediction for core histone macro-H2A.1 (O75367) · a predicted model of the same protein · chain C against A, TM-score 0.94
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 P68433
- Every structure of UniProt Q5T006
- Every structure of UniProt O75367
- Every structure of UniProt Q9D2U9
- Elsewhere: RCSB PDB 1U35 · PDBe 1U35 · UniProt P68433 · UniProt Q5T006 · UniProt O75367 · UniProt Q9D2U9
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