MolNFT v1 · #96027 · protein
Crystal structure of saccharomyces cerevisiae SFH3 complexed with phosphatidylinositol
4J7Q · Phosphatidylinositol transfer protein PDR16: “Crystal structure of saccharomyces cerevisiae SFH3 complexed with phosphatidylinositol”. X-ray diffraction, 1 ligand (B7N), 6 pockets (best druggability 0.89). MolNFT v1 #96027 on…
- PDB
- 4J7Q
- Type
- protein
- Length
- 644 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphatidylinositol transfer protein PDR16
- UniProt
- P53860
- Ligands
- B7N
- Pockets
- 6 · best druggability 0.89
Structure
x-ray diffraction · 2 distinct chains · 45% helix, 12% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphatidylinositol transfer protein PDR16 | protein | 322 | 45% helix, 12% strand | P53860 |
| B | Phosphatidylinositol transfer protein PDR16 | protein | 322 | 45% helix, 12% strand | P53860 |
Ligands and binding sites
- B7N · (1R)-2-{[(S)-hydroxy{[(1S,2R,3R,4S,5S,6R)-2,3,4,5,6-pentahydroxycyclohexyl]oxy}phosphoryl]oxy}-1-[(octadecanoyloxy)methyl]ethyl (9Z)-octadec-9-enoate · ligand · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 989 | 0.89 | 0.90 | 91 | B7N |
| 2 | 91 | 0.74 | 0.96 | 35 | empty |
| 3 | 116 | 0.62 | 0.87 | 29 | empty |
| 4 | 260 | 0.54 | 0.77 | 35 | empty |
| 5 | 233 | 0.53 | 0.77 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 976 Ų buried · 6 hydrogen bonds · protein-protein
Compared structures
- 4J7Q · Crystal structure of Saccharomyces cerevisiae Sfh3 complexed with phosphatidylinositol · the same entry in another collection · chain A against A, TM-score 1.00
- P53860 · AlphaFold monomer V2.0 prediction for phosphatidylinositol transfer protein PDR16 (P53860) · a predicted model of the same protein · chain B against A, TM-score 1.00
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 P53860
- Elsewhere: RCSB PDB 4J7Q · PDBe 4J7Q · UniProt P53860
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