Research workbench
Crystal structure of mammalian period-cryptochrome complex
Analyse Crystal structure of mammalian period-cryptochrome complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4U8H
- Type
- protein
- Length
- 1,138 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Cryptochrome-2; Period circadian protein homolog 2
- UniProt
- Q9R194, O54943
- Ligands
- ZN
- Pockets
- 17 · best druggability 0.85
Structure
x-ray diffraction · 2 distinct chains · 47% helix, 5% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Cryptochrome-2 | protein | 490 | 47% helix, 6% strand | Q9R194 |
| B, D | Period circadian protein homolog 2 | protein | 79 | 47% helix, 0% strand | O54943 |
Ligands and binding sites
- ZN · Zinc ion · metal · 2 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1085 | 0.85 | 0.86 | 93 | empty |
| 2 | 734 | 0.76 | 0.80 | 60 | empty |
| 3 | 635 | 0.73 | 0.80 | 58 | empty |
| 4 | 719 | 0.73 | 0.79 | 52 | empty |
| 5 | 558 | 0.67 | 0.77 | 43 | empty |
Interfaces
4 interfaces between chains.
- C–D · 3032 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 3004 Ų buried · 24 hydrogen bonds · protein-protein
- A–C · 533 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 440 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 4U8H · Crystal Structure of Mammalian Period-Cryptochrome Complex · 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 C against A, TM-score 0.98
- O54943 · AlphaFold monomer V2.0 prediction for period circadian protein homolog 2 (O54943) · a predicted model of the same protein · chain B against A, TM-score 0.43
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
- Every structure of UniProt O54943
- Elsewhere: RCSB PDB 4U8H · PDBe 4U8H · UniProt Q9R194 · UniProt O54943
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