Research workbench
Mammalian clock protein MPER2 - crystal structure of a pas domain fragment
Analyse Mammalian clock protein MPER2 - crystal structure of a pas domain fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3GDI
- Type
- protein
- Length
- 519 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Period circadian protein homolog 2
- UniProt
- O54943
- Pockets
- 10 · best druggability 0.79
Structure
x-ray diffraction · 2 distinct chains · 20% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Period circadian protein homolog 2 | protein | 269 | 20% helix, 32% strand | O54943 |
| B | Period circadian protein homolog 2 | protein | 250 | 21% helix, 32% strand | O54943 |
Pockets
10 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 599 | 0.79 | 0.85 | 61 | empty |
| 2 | 517 | 0.77 | 0.84 | 54 | empty |
| 3 | 302 | 0.55 | 0.76 | 39 | empty |
| 4 | 176 | 0.53 | 0.79 | 23 | empty |
| 5 | 65 | 0.49 | 0.83 | 13 | empty |
Interfaces
1 interface between chains.
- A–B · 1344 Ų buried · 4 hydrogen bonds · protein-protein
Compared structures
- 3GDI · Mammalian Clock Protein mPER2 - Crystal Structure of a PAS Domain Fragment · the same entry in another collection · chain A against A, TM-score 1.00
- O54943 · AlphaFold monomer V2.0 prediction for period circadian protein homolog 2 (O54943) · a predicted model of the same protein · chain A against A, TM-score 0.97
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 O54943
- Elsewhere: RCSB PDB 3GDI · PDBe 3GDI · UniProt O54943
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