MolNFT v1 · #16910 · protein
Crystal structure of the yeast px-domain protein GRD19P (sorting nexin 3) complexed to phosphatidylinosytol-3-phosphate.
1OCU: “Crystal structure of the yeast px-domain protein GRD19P (sorting nexin 3) complexed to…”. X-ray diffraction, 1 ligand (PIB), 3 pockets (best druggability 0.40). MolNFT v1 #16910 on GenesisL1: 3D structure, binding sites and pockets…
- PDB
- 1OCU
- Type
- protein
- Length
- 266 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Sorting nexin
- UniProt
- Q08826
- Ligands
- PIB
- Pockets
- 3 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 39% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Sorting nexin | protein | 134 | 40% helix, 21% strand | Q08826 |
| B | Sorting nexin | protein | 132 | 39% helix, 21% strand | Q08826 |
Ligands and binding sites
- PIB · 2-(butanoyloxy)-1-{[(hydroxy{[2,3,4,6-tetrahydroxy-5-(phosphonooxy)cyclohexyl]oxy}phosphoryl) oxy]methyl}ethyl butanoate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 66 | 0.40 | 0.80 | 13 | PIB |
| 2 | 58 | 0.39 | 0.80 | 13 | PIB |
| 3 | 56 | 0.25 | 0.72 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 520 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 modified (artifact).
Compared structures
- 1OCU · Crystal structure of the yeast PX-domain protein Grd19p (sorting nexin 3) complexed to… · the same entry in another collection · chain A against A, TM-score 1.00
- Q08826 · AlphaFold monomer V2.0 prediction for sorting nexin-3 (Q08826) · a predicted model of the same protein · chain B 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 Q08826
- Elsewhere: RCSB PDB 1OCU · PDBe 1OCU · UniProt Q08826
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