Research workbench
Unwinding the differences of the mammalian period clock proteins from crystal structure to cellular function
Analyse Unwinding the differences of the mammalian period clock proteins from crystal… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4DJ2
- Type
- protein
- Length
- 1,065 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Period circadian protein homolog 1
- UniProt
- O35973
- Pockets
- 18 · best druggability 0.78
Structure
x-ray diffraction · 4 distinct chains · 26% helix, 30% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Period circadian protein homolog 1 | protein | 276 | 27% helix, 30% strand | O35973 |
| B | Period circadian protein homolog 1 | protein | 279 | 27% helix, 32% strand | O35973 |
| C | Period circadian protein homolog 1 | protein | 264 | 24% helix, 28% strand | O35973 |
| D | Period circadian protein homolog 1 | protein | 246 | 24% helix, 30% strand | O35973 |
Pockets
18 pockets found on a 1 Å grid, 8 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1016 | 0.78 | 0.80 | 92 | empty |
| 2 | 665 | 0.67 | 0.76 | 60 | empty |
| 3 | 622 | 0.66 | 0.76 | 59 | empty |
| 4 | 96 | 0.65 | 0.90 | 24 | empty |
| 5 | 102 | 0.64 | 0.89 | 22 | empty |
Interfaces
5 interfaces between chains.
- A–C · 916 Ų buried · 2 hydrogen bonds · protein-protein
- B–D · 823 Ų buried · 3 hydrogen bonds · protein-protein
- B–C · 466 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 235 Ų buried · 5 hydrogen bonds · protein-protein
- C–D · 77 Ų buried · 0 hydrogen bonds · protein-protein
Compared structures
- 4DJ2 · Unwinding the Differences of the Mammalian PERIOD Clock Proteins from Crystal Structure… · the same entry in another collection · chain D against D, TM-score 1.00
- O35973 · AlphaFold monomer V2.0 prediction for period circadian protein homolog 1 (O35973) · a predicted model of the same protein · chain D 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 O35973
- Elsewhere: RCSB PDB 4DJ2 · PDBe 4DJ2 · UniProt O35973
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