Research workbench
Structure of the STRA6 receptor for retinol uptake in complex with calmodulin
Analyse Structure of the STRA6 receptor for retinol uptake in complex with calmodulin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5SY1
- Type
- protein
- Length
- 1,458 residues
- Chains
- 4
- Method
- electron microscopy
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Calmodulin; STRA6
- UniProt
- A4IGB6
- Ligands
- CLR, CA
- Pockets
- 20 · best druggability 0.78
Structure
electron microscopy · 2 distinct chains · 64% helix, 2% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, D | Calmodulin | protein | 147 | 54% helix, 3% strand | — |
| A, B | STRA6 | protein | 582 | 66% helix, 1% strand | A4IGB6 |
Ligands and binding sites
- CLR · Cholesterol · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 8 copies · chains 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, 13 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 639 | 0.78 | 0.83 | 38 | empty |
| 2 | 675 | 0.78 | 0.83 | 42 | empty |
| 3 | 70 | 0.64 | 0.92 | 16 | empty |
| 4 | 62 | 0.64 | 0.92 | 13 | empty |
| 5 | 337 | 0.63 | 0.79 | 46 | empty |
Interfaces
5 interfaces between chains.
- A–B · 5307 Ų buried · 34 hydrogen bonds · protein-protein
- B–D · 3414 Ų buried · 27 hydrogen bonds · protein-protein
- C–A · 3380 Ų buried · 29 hydrogen bonds · protein-protein
- C–B · 179 Ų buried · 1 hydrogen bond · protein-protein
- A–D · 157 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 5SY1 · Structure of the STRA6 receptor for retinol uptake in complex with calmodulin · the same entry in another collection · chain C against C, 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 A4IGB6
- Elsewhere: RCSB PDB 5SY1 · PDBe 5SY1 · UniProt A4IGB6
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