Research workbench
Structure of OSH6P in complex with phosphatidylinositol 4-phosphate
Analyse Structure of OSH6P in complex with phosphatidylinositol 4-phosphate in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4PH7
- Type
- protein
- Length
- 1,598 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Oxysterol-binding protein homolog 6
- UniProt
- Q02201
- Ligands
- 2Y5
- Pockets
- 20 · best druggability 0.86
Structure
x-ray diffraction · 4 distinct chains · 29% helix, 31% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Oxysterol-binding protein homolog 6 | protein | 401 | 28% helix, 32% strand | Q02201 |
| B | Oxysterol-binding protein homolog 6 | protein | 395 | 28% helix, 31% strand | Q02201 |
| C | Oxysterol-binding protein homolog 6 | protein | 395 | 29% helix, 31% strand | Q02201 |
| D | Oxysterol-binding protein homolog 6 | protein | 407 | 31% helix, 31% strand | Q02201 |
Ligands and binding sites
- 2Y5 · (2R)-1-{[(R)-hydroxy{[(1r,2r,3r,4r,5s,6r)-2,3,5,6-tetrahydroxy-4-(phosphonooxy) cyclohexyl]oxy}phosphoryl]oxy}-3-(octadecanoyloxy) propan-2-yl (5Z,8Z,11Z,14Z)-icosa-5,8,11,14-tetraenoate · ligand · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1038 | 0.86 | 0.88 | 117 | empty |
| 2 | 882 | 0.86 | 0.88 | 92 | 2Y5 |
| 3 | 976 | 0.86 | 0.87 | 92 | 2Y5 |
| 4 | 899 | 0.85 | 0.87 | 101 | 2Y5 |
| 5 | 892 | 0.85 | 0.86 | 86 | 2Y5 |
Interfaces
4 interfaces between chains.
- A–D · 1509 Ų buried · 23 hydrogen bonds · protein-protein
- A–C · 168 Ų buried · 4 hydrogen bonds · protein-protein
- A–B · 158 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 23 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4PH7 · Structure of Osh6p in complex with phosphatidylinositol 4-phosphate · the same entry in another collection · chain D against D, TM-score 1.00
- Q02201 · AlphaFold monomer V2.0 prediction for oxysterol-binding protein homolog 6 (Q02201) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q02201
- Elsewhere: RCSB PDB 4PH7 · PDBe 4PH7 · UniProt Q02201
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