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Alternative crystal structure of mouse cryptochrome 2 in complex with TH301 compound
Analyse Alternative crystal structure of mouse cryptochrome 2 in complex with TH301… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7EJ9
- Type
- protein
- Length
- 952 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cryptochrome-2
- UniProt
- Q9R194
- Ligands
- DYX
- Pockets
- 8 · best druggability 0.76
Structure
x-ray diffraction · 2 distinct chains · 50% helix, 7% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Cryptochrome-2 | protein | 482 | 51% helix, 7% strand | Q9R194 |
| B | Cryptochrome-2 | protein | 470 | 50% helix, 7% strand | Q9R194 |
Ligands and binding sites
- DYX · 1-(4-chlorophenyl)-N-[2-(4-methoxyphenyl)-5,5-bis(oxidanylidene)-4,6-dihydrothieno[3,4-c]pyrazol-3-yl]cyclopentane-1-carboxamide · ligand · 2 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, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 716 | 0.76 | 0.80 | 76 | DYX |
| 2 | 642 | 0.75 | 0.81 | 54 | DYX |
| 3 | 621 | 0.74 | 0.80 | 53 | empty |
| 4 | 602 | 0.73 | 0.80 | 43 | empty |
| 5 | 219 | 0.48 | 0.74 | 36 | empty |
Interfaces
1 interface between chains.
- A–B · 704 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7EJ9 · Alternative crystal structure of mouse Cryptochrome 2 in complex with TH301 compound · the same entry in another collection · chain A against A, TM-score 1.00
- Q9R194 · AlphaFold monomer V2.0 prediction for cryptochrome-2 (Q9R194) · a predicted model of the same protein · chain B against A, TM-score 0.99
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 Q9R194
- Elsewhere: RCSB PDB 7EJ9 · PDBe 7EJ9 · UniProt Q9R194
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