MolNFT v1 · #134233 · protein
Structure of the STRA6 receptor for retinol uptake in complex with calmodulin
5SY1: “Structure of the STRA6 receptor for retinol uptake in complex with calmodulin”. Electron microscopy, 2 ligands (CLR, CA), 20 pockets (best druggability 0.78). MolNFT v1 #134233 on GenesisL1: 3D structure, binding sites and pockets…
- 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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