MolNFT v1 · #123976 · protein
Crystal structure of wd repeat-containing protein 20
5K19: “Crystal structure of wd repeat-containing protein 20”. X-ray diffraction, 1 ligand (SO4), 11 pockets (best druggability 0.78). MolNFT v1 #123976 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5K19
- Type
- protein
- Length
- 1,108 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Wd repeat-containing protein 20
- UniProt
- Q8TBZ3
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 2% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Wd repeat-containing protein 20 | protein | 376 | 2% helix, 48% strand | Q8TBZ3 |
| B | Wd repeat-containing protein 20 | protein | 373 | 2% helix, 48% strand | Q8TBZ3 |
| C | Wd repeat-containing protein 20 | protein | 359 | 1% helix, 51% strand | Q8TBZ3 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1041 | 0.78 | 0.80 | 75 | empty |
| 2 | 890 | 0.77 | 0.80 | 63 | GOL |
| 3 | 875 | 0.76 | 0.79 | 60 | empty |
| 4 | 87 | 0.41 | 0.78 | 21 | empty |
| 5 | 154 | 0.41 | 0.73 | 25 | GOL |
Interfaces
1 interface between chains.
- A–B · 153 Ų buried · 0 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 Q8TBZ3
- Elsewhere: RCSB PDB 5K19 · PDBe 5K19 · UniProt Q8TBZ3
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