Research workbench
Crystal structure analysis of the phd domain of the transcription coactivator pygophus
Analyse Crystal structure analysis of the phd domain of the transcription coactivator… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2DX8
- Type
- protein
- Length
- 120 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Pygopus homolog 1
- UniProt
- Q9D0P5
- Ligands
- ZN
- Pockets
- 2 · best druggability 0.32
Structure
x-ray diffraction · 1 distinct chain · 23% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Pygopus homolog 1 | protein | 60 | 23% helix, 18% strand | Q9D0P5 |
Ligands and binding sites
- ZN · Zinc ion · metal · 4 copies · chains A, B
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 | 53 | 0.32 | 0.77 | 18 | empty |
| 2 | 55 | 0.31 | 0.76 | 12 | empty |
Interfaces
1 interface between chains.
- A–B · 483 Ų buried · 7 hydrogen bonds · protein-protein
Compared structures
- 2DX8 · Crystal Structure Analysis of the PHD domain of the Transcription Coactivator Pygophus · the same entry in another collection · chain A against A, TM-score 1.00
- Q9D0P5 · AlphaFold monomer V2.0 prediction for pygopus homolog 1 (Q9D0P5) · a predicted model of the same protein · chain A against A, TM-score 0.96
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 Q9D0P5
- Elsewhere: RCSB PDB 2DX8 · PDBe 2DX8 · UniProt Q9D0P5
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