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
- 2X4W
- Type
- protein
- Length
- 138 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Peregrin; Histone H3.2
- UniProt
- P55201, Q71DI3
- Pockets
- 2 · best druggability 0.43
Structure
x-ray diffraction · 2 distinct chains · 34% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Peregrin | protein | 125 | 38% helix, 22% strand | P55201 |
| B | Histone H3.2 | protein | 13 | 0% helix, 8% strand | Q71DI3 |
Ligands and binding sites
- FMT · Formic acid · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 92 | 0.43 | 0.79 | 15 | empty |
| 2 | 60 | 0.28 | 0.73 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 689 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (methylation).
Compared structures
- 2X4W · Molecular basis of Histone H3K36me3 recognition by the PWWP domain of BRPF1. · the same entry in another collection · chain A against A, TM-score 1.00
- P55201 · AlphaFold monomer V2.0 prediction for peregrin (P55201) · a predicted model of the same protein · chain A against A, TM-score 0.97
- Q71DI3 · AlphaFold monomer V2.0 prediction for histone H3.2 (Q71DI3) · a predicted model of the same protein · chain B against A, TM-score 0.33
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 2X4W · PDBe 2X4W · UniProt P55201 · UniProt Q71DI3
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