Research workbench
PHF2 jumonji domain-nog complex
Analyse PHF2 jumonji domain-nog complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3PU3
- Type
- protein
- Length
- 724 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phd finger protein 2
- UniProt
- O75151
- Ligands
- OGA
- Pockets
- 11 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 41% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phd finger protein 2 | protein | 363 | 40% helix, 21% strand | O75151 |
| B | Phd finger protein 2 | protein | 361 | 41% helix, 21% strand | O75151 |
Ligands and binding sites
- OGA · N-oxalylglycine · ligand · 2 copies · chains A, B
- EDO · 1,2-ethanediol · additive · 43 copies · chains A, B
- GOL · Glycerol · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 487 | 0.77 | 0.85 | 50 | OGA, EDO |
| 2 | 555 | 0.77 | 0.84 | 54 | OGA, EDO |
| 3 | 278 | 0.63 | 0.81 | 36 | EDO |
| 4 | 96 | 0.52 | 0.83 | 22 | EDO, GOL |
| 5 | 95 | 0.50 | 0.82 | 21 | EDO |
Interfaces
1 interface between chains.
- A–B · 457 Ų buried · 4 hydrogen bonds · protein-protein
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 O75151
- Elsewhere: RCSB PDB 3PU3 · PDBe 3PU3 · UniProt O75151
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