MolNFT v1 · #114134 · protein + DNA
The crystal structure of the H2AZ nucleosome with H3.3.
5B33 · Histone H3.3: “The crystal structure of the H2AZ nucleosome with H3.3.”. X-ray diffraction, 20 pockets (best druggability 0.81). MolNFT v1 #114134 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5B33
- Type
- protein + DNA
- Length
- 1,042 residues
- Chains
- 10
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Histone H3.3; Histone H4; Histone H2A.Z; Histone H2B type 1-J; DNA (146-mer)
- UniProt
- P84243, P62805, P0C0S5, P06899
- Pockets
- 20 · best druggability 0.81
Structure
x-ray diffraction · 8 distinct chains · 62% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Histone H3.3 | protein | 97 | 64% helix, 4% strand | P84243 |
| B | Histone H4 | protein | 78 | 63% helix, 8% strand | P62805 |
| C | Histone H2A.Z | protein | 105 | 59% helix, 6% strand | P0C0S5 |
| D, H | Histone H2B type 1-J | protein | 92 | 73% helix, 4% strand | P06899 |
| E | Histone H3.3 | protein | 98 | 64% helix, 4% strand | P84243 |
| F | Histone H4 | protein | 84 | 60% helix, 7% strand | P62805 |
| G | Histone H2A.Z | protein | 104 | 55% helix, 6% strand | P0C0S5 |
| 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 | 823 | 0.81 | 0.84 | 92 | empty |
| 2 | 485 | 0.71 | 0.81 | 47 | empty |
| 3 | 546 | 0.69 | 0.79 | 44 | empty |
| 4 | 561 | 0.69 | 0.79 | 45 | empty |
| 5 | 355 | 0.67 | 0.82 | 35 | empty |
Interfaces
36 interfaces between chains.
- I–J · 6361 Ų buried · 535 hydrogen bonds · nucleic-nucleic
- E–F · 2686 Ų buried · 25 hydrogen bonds · protein-protein
- G–H · 2675 Ų buried · 31 hydrogen bonds · protein-protein
- C–D · 2641 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2530 Ų buried · 22 hydrogen bonds · protein-protein
Compared structures
- 5B33 · The crystal structure of the H2AZ nucleosome with H3.3. · the same entry in another collection · chain J against J, TM-score 1.00
- P84243 · AlphaFold monomer V2.0 prediction for histone H3.3 (P84243) · a predicted model of the same protein · chain A against A, TM-score 0.99
- P0C0S5 · AlphaFold monomer V2.0 prediction for histone H2A.Z (P0C0S5) · a predicted model of the same protein · chain G against A, TM-score 0.99
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 P84243
- Every structure of UniProt P62805
- Every structure of UniProt P0C0S5
- Every structure of UniProt P06899
- Elsewhere: RCSB PDB 5B33 · PDBe 5B33 · UniProt P84243 · UniProt P62805 · UniProt P0C0S5 · UniProt P06899
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