Research workbench
Crystal structure of the clock transcription domain EXON19 in complex with a repressor
Analyse Crystal structure of the clock transcription domain EXON19 in complex with a… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5VJI
- Type
- protein
- Length
- 296 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Circadian locomoter output cycles protein kaput; Clock-interacting pacemaker
- EC
- 2.3.1.48
- UniProt
- O08785, Q8R0W1
- Pockets
- 4 · best druggability 0.67
Structure
x-ray diffraction · 6 distinct chains · 88% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 50 | 84% helix, 0% strand | O08785 |
| B | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 42 | 93% helix, 0% strand | O08785 |
| C | Clock-interacting pacemaker | protein | 57 | 84% helix, 0% strand | Q8R0W1 |
| D | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 42 | 95% helix, 0% strand | O08785 |
| E | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 49 | 86% helix, 0% strand | O08785 |
| F | Clock-interacting pacemaker | protein | 56 | 89% helix, 0% strand | Q8R0W1 |
Pockets
4 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 199 | 0.67 | 0.85 | 26 | empty |
| 2 | 249 | 0.67 | 0.83 | 36 | empty |
| 3 | 227 | 0.55 | 0.78 | 26 | empty |
| 4 | 95 | 0.43 | 0.78 | 19 | empty |
Interfaces
11 interfaces between chains.
- E–F · 1009 Ų buried · 8 hydrogen bonds · protein-protein
- D–F · 983 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 908 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 850 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 846 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 modified (engineered).
Compared structures
- 5VJI · Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor · the same entry in another collection · chain F against F, TM-score 1.00
- Q8R0W1 · AlphaFold monomer V2.0 prediction for clock-interacting pacemaker (Q8R0W1) · a predicted model of the same protein · chain F against A, TM-score 0.89
- O08785 · AlphaFold monomer V2.0 prediction for circadian locomoter output cycles protein kaput… · a predicted model of the same protein · chain D against A, TM-score 0.85
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 O08785
- Every structure of UniProt Q8R0W1
- Elsewhere: RCSB PDB 5VJI · PDBe 5VJI · UniProt O08785 · UniProt Q8R0W1
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