MolNFT v1 · #53774 · protein
Molecular basis of histone H3K36ME3 recognition by the pwwp domain of BRPF1.
2X4X · Peregrin: “Molecular basis of histone H3K36ME3 recognition by the pwwp domain of BRPF1.”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.68). MolNFT v1 #53774 on GenesisL1: 3D structure, binding sites and pockets…
- 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
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