MolNFT v1 · #23537 · protein + DNA
Crystal structure of the nucleosome core particle containing the histone domain of MACROH2A
1U35 · Alpha-satellite DNA: “Crystal structure of the nucleosome core particle containing the histone domain of MACROH2A”. X-ray diffraction, 20 pockets (best druggability 0.78). MolNFT v1 #23537 on GenesisL1: 3D structure, binding sites…
- 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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