MolNFT v1 · #114086 · protein + DNA
The mouse nucleosome structure containing H3.1
5B1M · Histone H3.1: “The mouse nucleosome structure containing H3.1”. X-ray diffraction, 20 pockets (best druggability 0.75). MolNFT v1 #114086 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5B1M
- Type
- protein + DNA
- Length
- 1,048 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.1; Histone H4; Histone H2A type 1; Histone H2B type 3-a; DNA (146-mer)
- UniProt
- P68433, P62806, P22752, Q9D2U9
- Pockets
- 20 · best druggability 0.75
Structure
x-ray diffraction · 9 distinct chains · 64% helix, 6% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.1 | protein | 97 | 65% helix, 4% strand | P68433 |
| B | Histone H4 | protein | 78 | 63% helix, 9% strand | P62806 |
| C | Histone H2A type 1 | protein | 108 | 56% helix, 6% strand | P22752 |
| D | Histone H2B type 3-a | protein | 94 | 72% helix, 4% strand | Q9D2U9 |
| E | Histone H3.1 | protein | 99 | 65% helix, 4% strand | P68433 |
| F | Histone H4 | protein | 84 | 60% helix, 8% strand | P62806 |
| G | Histone H2A type 1 | protein | 104 | 57% helix, 7% strand | P22752 |
| H | Histone H2B type 3-a | protein | 92 | 74% 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 | 397 | 0.75 | 0.86 | 49 | empty |
| 2 | 203 | 0.72 | 0.89 | 31 | empty |
| 3 | 744 | 0.70 | 0.77 | 58 | empty |
| 4 | 141 | 0.67 | 0.89 | 27 | empty |
| 5 | 583 | 0.67 | 0.77 | 30 | empty |
Interfaces
35 interfaces between chains.
- I–J · 6450 Ų buried · 528 hydrogen bonds · nucleic-nucleic
- E–F · 2746 Ų buried · 28 hydrogen bonds · protein-protein
- C–D · 2628 Ų buried · 22 hydrogen bonds · protein-protein
- G–H · 2583 Ų buried · 24 hydrogen bonds · protein-protein
- A–B · 2471 Ų buried · 21 hydrogen bonds · protein-protein
Compared structures
- 5B1M · The mouse nucleosome structure containing H3.1 · the same entry in another collection · chain J against J, 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 0.99
- P62806 · AlphaFold monomer V2.0 prediction for histone H4 (P62806) · a predicted model of the same protein · chain F 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 P68433
- Every structure of UniProt P62806
- Every structure of UniProt P22752
- Every structure of UniProt Q9D2U9
- Elsewhere: RCSB PDB 5B1M · PDBe 5B1M · UniProt P68433 · UniProt P62806 · UniProt P22752 · UniProt Q9D2U9
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