Research workbench
Crystal structure of the genetically encoded calcium indicator RGECO1
Analyse Crystal structure of the genetically encoded calcium indicator RGECO1 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4I2Y
- Type
- protein
- Length
- 759 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- RGECO1
- UniProt
- Q6LDG3, Q9U6Y8, P62161
- Ligands
- NRQ, CA
- Pockets
- 10 · best druggability 0.83
Structure
x-ray diffraction · 2 distinct chains · 30% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | RGECO1 | protein | 381 | 31% helix, 34% strand | Q6LDG3, Q9U6Y8, P62161 |
| B | RGECO1 | protein | 378 | 30% helix, 34% strand | Q6LDG3, Q9U6Y8, P62161 |
Ligands and binding sites
- NRQ · {(4Z)-4-(4-hydroxybenzylidene)-2-[3-(methylthio) propanimidoyl]-5-oxo-4,5-dihydro-1H-imidazol-1-yl}acetic acid · ligand · 2 copies · chains A, B
- CA · Calcium ion · metal · 8 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
10 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 490 | 0.83 | 0.89 | 62 | NRQ |
| 2 | 515 | 0.80 | 0.87 | 60 | NRQ |
| 3 | 674 | 0.78 | 0.83 | 102 | empty |
| 4 | 183 | 0.57 | 0.81 | 35 | empty |
| 5 | 212 | 0.51 | 0.76 | 30 | empty |
Interfaces
1 interface between chains.
- A–B · 782 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 cofactor (chromophore).
Compared structures
- 4I2Y · Crystal Structure of the genetically encoded calcium indicator RGECO1 · the same entry in another collection · chain A against A, TM-score 1.00
- Q9U6Y8 · AlphaFold monomer V2.0 prediction for red fluorescent protein DRFP583 (Q9U6Y8) · a predicted model of the same protein · chain B against A, TM-score 0.37
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 Q6LDG3
- Every structure of UniProt Q9U6Y8
- Every structure of UniProt P62161
- Elsewhere: RCSB PDB 4I2Y · PDBe 4I2Y · UniProt Q6LDG3 · UniProt Q9U6Y8 · UniProt P62161
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