Research workbench
Crystal structure of the human PYGO2 phd finger in complex with the B9L HD1 domain
Analyse Crystal structure of the human PYGO2 phd finger in complex with the B9L HD1… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2XB1
- Type
- protein
- Length
- 193 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pygopus homolog 2, B-cell CLL/LYMPHOMA 9-like protein
- UniProt
- Q9BRQ0, Q86UU0
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.38
Structure
x-ray diffraction · 2 distinct chains · 38% helix, 15% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Pygopus homolog 2, B-cell CLL/LYMPHOMA 9-like protein | protein | 96 | 39% helix, 15% strand | Q9BRQ0, Q86UU0 |
| C | Pygopus homolog 2, B-cell CLL/LYMPHOMA 9-like protein | protein | 97 | 38% helix, 14% strand | Q9BRQ0, Q86UU0 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, C
- GOL · Glycerol · additive · 2 copies · chains A, C
- PEG · Di(hydroxyethyl)ether · additive · chains C
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 | 99 | 0.38 | 0.75 | 21 | empty |
| 2 | 60 | 0.34 | 0.77 | 11 | empty |
Interfaces
1 interface between chains.
- A–C · 376 Ų buried · 5 hydrogen bonds · protein-protein
Compared structures
- 2XB1 · Crystal structure of the human Pygo2 PHD finger in complex with the B9L HD1 domain · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BRQ0 · AlphaFold monomer V2.0 prediction for pygopus homolog 2 (Q9BRQ0) · a predicted model of the same protein · chain C against A, TM-score 0.65
- Q86UU0 · AlphaFold monomer V2.0 prediction for B-cell CLL/LYMPHOMA 9-like protein (Q86UU0) · a predicted model of the same protein · chain C against A, TM-score 0.25
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 Q9BRQ0
- Every structure of UniProt Q86UU0
- Elsewhere: RCSB PDB 2XB1 · PDBe 2XB1 · UniProt Q9BRQ0 · UniProt Q86UU0
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