MolNFT v1 · #139646 · protein + DNA
The mouse nucleosome structure containing H2A, H2B TYPE3-a, H3.3, and H4
5XM0 · Histone H3.3: “The mouse nucleosome structure containing H2A, H2B TYPE3-a, H3.3, and H4”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #139646 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5XM0
- Type
- protein + DNA
- Length
- 1,043 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.3; Histone H4; Histone H2A type 1-B; Histone H2B type 3-a; DNA (146-mer)
- UniProt
- P84244, P62806, C0HKE1, Q9D2U9
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 63% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Histone H3.3 | protein | 97 | 63% helix, 4% strand | P84244 |
| B | Histone H4 | protein | 78 | 63% helix, 9% strand | P62806 |
| C | Histone H2A type 1-B | protein | 105 | 58% helix, 7% strand | C0HKE1 |
| D | Histone H2B type 3-a | protein | 94 | 73% helix, 4% strand | Q9D2U9 |
| F | Histone H4 | protein | 84 | 60% helix, 8% strand | P62806 |
| G | Histone H2A type 1-B | protein | 104 | 56% helix, 7% strand | C0HKE1 |
| H | Histone H2B type 3-a | protein | 92 | 73% helix, 4% strand | Q9D2U9 |
| I, J | DNA (146-mer) | dna | 146 | — | — |
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 | 791 | 0.81 | 0.84 | 70 | empty |
| 2 | 524 | 0.76 | 0.84 | 54 | empty |
| 3 | 494 | 0.74 | 0.83 | 52 | empty |
| 4 | 1071 | 0.72 | 0.76 | 80 | empty |
| 5 | 717 | 0.69 | 0.77 | 50 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6378 Ų buried · 581 hydrogen bonds · nucleic-nucleic
- E–F · 2639 Ų buried · 27 hydrogen bonds · protein-protein
- C–D · 2622 Ų buried · 26 hydrogen bonds · protein-protein
- G–H · 2605 Ų buried · 20 hydrogen bonds · protein-protein
- A–B · 2536 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5XM0 · The mouse nucleosome structure containing H2A, H2B type3-A, H3.3, and H4 · the same entry in another collection · chain J against J, TM-score 1.00
- P84244 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84244) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P62806 · AlphaFold monomer V2.0 prediction for histone H4 (P62806) · a predicted model of the same protein · chain B 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 P84244
- Every structure of UniProt P62806
- Every structure of UniProt C0HKE1
- Every structure of UniProt Q9D2U9
- Elsewhere: RCSB PDB 5XM0 · PDBe 5XM0 · UniProt P84244 · UniProt P62806 · UniProt C0HKE1 · UniProt Q9D2U9
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