Research workbench
Crystal structure of the transmembrane domain and linker region of salpingoeca rosetta rhodopsin phosphodiesterase
Analyse Crystal structure of the transmembrane domain and linker region of salpingoeca… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7D7Q
- Type
- protein
- Length
- 588 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Phosphodiesterase
- EC
- 3.1.4.-
- UniProt
- F2TZN0
- Ligands
- RET
- Pockets
- 8 · best druggability 0.81
Structure
x-ray diffraction · 2 distinct chains · 77% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Phosphodiesterase (EC 3.1.4.-) | protein | 278 | 79% helix, 2% strand | F2TZN0 |
| B | Phosphodiesterase (EC 3.1.4.-) | protein | 310 | 75% helix, 1% strand | F2TZN0 |
Ligands and binding sites
- RET · Retinal · ligand · 2 copies · chains A, B
- OLC · (2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate · additive · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 157 | 0.81 | 0.96 | 27 | RET |
| 2 | 138 | 0.78 | 0.95 | 23 | RET |
| 3 | 260 | 0.66 | 0.83 | 32 | OLC |
| 4 | 78 | 0.35 | 0.76 | 14 | empty |
| 5 | 65 | 0.35 | 0.77 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 1362 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 2 cofactor (retinal Schiff base).
Compared structures
- 7D7Q · Crystal structure of the transmembrane domain and linker region of Salpingoeca rosetta… · the same entry in another collection · chain A 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 F2TZN0
- Elsewhere: RCSB PDB 7D7Q · PDBe 7D7Q · UniProt F2TZN0
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