Research workbench
Decoding of methylated histone H3 tail by the pygo-BCL9 wnt signaling complex
Analyse Decoding of methylated histone H3 tail by the pygo-BCL9 wnt signaling complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2VPG
- Type
- protein
- Length
- 198 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pygopus homolog 1; B-cell CLL/LYMPHOMA 9 protein; Histone H3 tail
- UniProt
- Q9Y3Y4, O00512
- Ligands
- ZN
- Pockets
- 3 · best druggability 0.43
Structure
x-ray diffraction · 4 distinct chains · 30% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pygopus homolog 1 | protein | 61 | 30% helix, 20% strand | Q9Y3Y4 |
| B, D | B-cell CLL/LYMPHOMA 9 protein | protein | 30 | 40% helix, 10% strand | O00512 |
| C | Pygopus homolog 1 | protein | 63 | 29% helix, 19% strand | Q9Y3Y4 |
| P, R | Histone H3 tail | protein | 7 | 0% helix, 14% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 158 | 0.43 | 0.74 | 27 | empty |
| 2 | 100 | 0.35 | 0.73 | 21 | empty |
| 3 | 64 | 0.30 | 0.74 | 17 | empty |
Interfaces
5 interfaces between chains.
- A–B · 621 Ų buried · 9 hydrogen bonds · protein-protein
- C–D · 601 Ų buried · 9 hydrogen bonds · protein-protein
- C–R · 516 Ų buried · 10 hydrogen bonds · protein-protein
- A–P · 511 Ų buried · 10 hydrogen bonds · protein-protein
- A–C · 232 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 4 modified (methylation, nonstandard).
Compared structures
- 2VPG · Decoding of methylated histone H3 tail by the Pygo-BCL9 Wnt signaling complex · the same entry in another collection · chain B against B, TM-score 1.00
- Q9Y3Y4 · AlphaFold monomer V2.0 prediction for pygopus homolog 1 (Q9Y3Y4) · a predicted model of the same protein · chain C against A, TM-score 0.95
- O00512 · AlphaFold monomer V2.0 prediction for B-cell CLL/LYMPHOMA 9 protein (O00512) · a predicted model of the same protein · chain B against A, TM-score 0.63
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 Q9Y3Y4
- Every structure of UniProt O00512
- Elsewhere: RCSB PDB 2VPG · PDBe 2VPG · UniProt Q9Y3Y4 · UniProt O00512
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