Research workbench
Structure of fully modified farnesylated INPP5E peptide in complex with PDE6D
Analyse Structure of fully modified farnesylated INPP5E peptide in complex with PDE6D in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5F2U
- Type
- protein
- Length
- 307 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta…
- UniProt
- O43924
- Ligands
- FAR
- Pockets
- 3 · best druggability 0.81
Structure
x-ray diffraction · 3 distinct chains · 15% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta | protein | 149 | 15% helix, 59% strand | O43924 |
| B | Retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic phosphodiesterase subunit delta | protein | 148 | 16% helix, 59% strand | O43924 |
| C, D | Phosphatidylinositol 4,5-bisphosphate 5-phosphatase, S- farnesyl-L-cysteine methyl ester | protein | 5 | 0% helix, 20% strand | — |
Ligands and binding sites
- FAR · Farnesyl · ligand · 2 copies · chains A, C, B, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 160 | 0.81 | 0.96 | 23 | FAR |
| 2 | 152 | 0.81 | 0.96 | 23 | FAR |
| 3 | 156 | 0.51 | 0.79 | 21 | empty |
Interfaces
3 interfaces between chains.
- B–D · 503 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 500 Ų buried · 7 hydrogen bonds · protein-protein
- A–B · 377 Ų buried · 3 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 lipid, 2 modified (farnesylation, nonstandard).
Compared structures
- 5F2U · Structure of Fully modified farnesylated INPP5E Peptide in complex with PDE6D · the same entry in another collection · chain A against A, TM-score 1.00
- O43924 · AlphaFold monomer V2.0 prediction for retinal rod rhodopsin-sensitive cgmp 3',5'-cyclic… · a predicted model of the same protein · chain A 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 O43924
- Elsewhere: RCSB PDB 5F2U · PDBe 5F2U · UniProt O43924
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