Research workbench
Molecular basis of histone H3K36ME3 recognition by the pwwp domain of BRPF1.
Analyse Molecular basis of histone H3K36ME3 recognition by the pwwp domain of BRPF1. in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2X4X
- Type
- protein
- Length
- 548 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peregrin; Histone H3.2
- UniProt
- P55201, Q71DI3
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.68
Structure
x-ray diffraction · 6 distinct chains · 34% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, E | Peregrin | protein | 126 | 37% helix, 24% strand | P55201 |
| B | Histone H3.2 | protein | 14 | 0% helix, 7% strand | Q71DI3 |
| C | Peregrin | protein | 125 | 38% helix, 24% strand | P55201 |
| D, H | Histone H3.2 | protein | 12 | 0% helix, 8% strand | Q71DI3 |
| F | Histone H3.2 | protein | 11 | 0% helix, 9% strand | Q71DI3 |
| G | Peregrin | protein | 122 | 38% helix, 23% strand | P55201 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 922 | 0.68 | 0.74 | 50 | empty |
| 2 | 104 | 0.40 | 0.76 | 19 | empty |
| 3 | 90 | 0.40 | 0.77 | 15 | empty |
| 4 | 101 | 0.39 | 0.76 | 17 | empty |
| 5 | 123 | 0.39 | 0.74 | 20 | empty |
Interfaces
8 interfaces between chains.
- A–B · 726 Ų buried · 6 hydrogen bonds · protein-protein
- C–D · 687 Ų buried · 7 hydrogen bonds · protein-protein
- G–H · 687 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 648 Ų buried · 7 hydrogen bonds · protein-protein
- A–E · 417 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (methylation).
Compared structures
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 P55201
- Every structure of UniProt Q71DI3
- Elsewhere: RCSB PDB 2X4X · PDBe 2X4X · UniProt P55201 · UniProt Q71DI3
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.