MolNFT v1 · #137289 · protein
Crystal structure of the clock transcription domain EXON19 in complex with a repressor
5VJX · Clock-interacting pacemaker: “Crystal structure of the clock transcription domain EXON19 in complex with a repressor”. X-ray diffraction, 19 pockets (best druggability 0.82). MolNFT v1 #137289 on GenesisL1: 3D structure, binding…
- PDB
- 5VJX
- Type
- protein
- Length
- 1,494 residues
- Chains
- 30
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Clock-interacting pacemaker; Circadian locomoter output cycles protein kaput
- EC
- 2.3.1.48
- UniProt
- Q8R0W1, O08785
- Pockets
- 19 · best druggability 0.82
Structure
x-ray diffraction · 24 distinct chains · 85% helix, 0% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Clock-interacting pacemaker | protein | 55 | 87% helix, 0% strand | Q8R0W1 |
| B | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 39 | 92% helix, 0% strand | O08785 |
| C | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 37 | 92% helix, 0% strand | O08785 |
| D | Clock-interacting pacemaker | protein | 63 | 81% helix, 0% strand | Q8R0W1 |
| E, V | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 49 | 80% helix, 0% strand | O08785 |
| F | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 44 | 93% helix, 0% strand | O08785 |
| G, U | Clock-interacting pacemaker | protein | 63 | 86% helix, 0% strand | Q8R0W1 |
| H | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 51 | 80% helix, 0% strand | O08785 |
| I | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 47 | 83% helix, 0% strand | O08785 |
| J, M, R | Clock-interacting pacemaker | protein | 64 | 81% helix, 0% strand | Q8R0W1 |
| K | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 43 | 88% helix, 0% strand | O08785 |
| L | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 49 | 84% helix, 0% strand | O08785 |
| N | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 42 | 83% helix, 0% strand | O08785 |
| O | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 48 | 88% helix, 0% strand | O08785 |
| S, W | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 50 | 86% helix, 0% strand | O08785 |
| T | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 44 | 89% helix, 0% strand | O08785 |
| X | Clock-interacting pacemaker | protein | 62 | 89% helix, 0% strand | Q8R0W1 |
| Y | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 46 | 89% helix, 0% strand | O08785 |
| Z | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 36 | 83% helix, 0% strand | O08785 |
| a | Clock-interacting pacemaker | protein | 51 | 65% helix, 0% strand | Q8R0W1 |
| b, f | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 47 | 83% helix, 0% strand | O08785 |
| c | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 38 | 87% helix, 0% strand | O08785 |
| d | Clock-interacting pacemaker | protein | 45 | 87% helix, 0% strand | Q8R0W1 |
| e | Circadian locomoter output cycles protein kaput (EC 2.3.1.48) | protein | 44 | 82% helix, 0% strand | O08785 |
Pockets
19 pockets found on a 1 Å grid, 14 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1116 | 0.82 | 0.83 | 104 | empty |
| 2 | 1012 | 0.77 | 0.79 | 96 | empty |
| 3 | 243 | 0.71 | 0.86 | 27 | empty |
| 4 | 788 | 0.69 | 0.76 | 67 | empty |
| 5 | 260 | 0.66 | 0.83 | 37 | empty |
Interfaces
74 interfaces between chains.
- U–V · 1053 Ų buried · 5 hydrogen bonds · protein-protein
- G–H · 1040 Ų buried · 6 hydrogen bonds · protein-protein
- U–W · 1002 Ų buried · 7 hydrogen bonds · protein-protein
- G–I · 972 Ų buried · 9 hydrogen bonds · protein-protein
- D–F · 953 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 73 modified (engineered).
Compared structures
- 5VJX · Crystal structure of the CLOCK Transcription Domain Exon19 in Complex with a Repressor · the same entry in another collection · chain K against K, TM-score 1.00
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 Q8R0W1
- Every structure of UniProt O08785
- Elsewhere: RCSB PDB 5VJX · PDBe 5VJX · UniProt Q8R0W1 · UniProt O08785
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