MolNFT v1 · #161074 · protein
Crystal structure of spoc domain of human phd-finger protein 3 (PHF3)
6Q2V · Phd finger protein 3: “Crystal structure of spoc domain of human phd-finger protein 3 (PHF3)”. X-ray diffraction, 20 pockets (best druggability 0.80). MolNFT v1 #161074 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6Q2V
- Type
- protein
- Length
- 1,174 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phd finger protein 3
- UniProt
- Q92576
- Pockets
- 20 · best druggability 0.80
Structure
x-ray diffraction · 5 distinct chains · 24% helix, 38% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C, D | Phd finger protein 3 | protein | 149 | 25% helix, 40% strand | Q92576 |
| B | Phd finger protein 3 | protein | 148 | 24% helix, 38% strand | Q92576 |
| E, F | Phd finger protein 3 | protein | 145 | 21% helix, 40% strand | Q92576 |
| G | Phd finger protein 3 | protein | 143 | 23% helix, 36% strand | Q92576 |
| H | Phd finger protein 3 | protein | 146 | 25% helix, 36% strand | Q92576 |
Ligands and binding sites
- GOL · Glycerol · additive · 2 copies · chains B, C, E, F
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 756 | 0.80 | 0.84 | 74 | GOL |
| 2 | 499 | 0.63 | 0.76 | 53 | empty |
| 3 | 499 | 0.61 | 0.75 | 49 | empty |
| 4 | 114 | 0.54 | 0.83 | 24 | empty |
| 5 | 168 | 0.50 | 0.78 | 27 | empty |
Interfaces
14 interfaces between chains.
- D–E · 710 Ų buried · 8 hydrogen bonds · protein-protein
- A–F · 670 Ų buried · 10 hydrogen bonds · protein-protein
- C–G · 609 Ų buried · 7 hydrogen bonds · protein-protein
- C–F · 583 Ų buried · 13 hydrogen bonds · protein-protein
- D–H · 583 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 24 modified (engineered).
Compared structures
- 6Q2V · Crystal structure of SPOC domain of human PHD-finger protein 3 (PHF3) · the same entry in another collection · chain H against H, TM-score 1.00
- Q92576 · AlphaFold monomer V2.0 prediction for phd finger protein 3 (Q92576) · a predicted model of the same protein · chain H against A, TM-score 0.98
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 Q92576
- Elsewhere: RCSB PDB 6Q2V · PDBe 6Q2V · UniProt Q92576
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