Research workbench
Crystal structure of an arabidopsis WD40 domain in complex with photoreceptor
Analyse Crystal structure of an arabidopsis WD40 domain in complex with photoreceptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QTQ
- Type
- protein
- Length
- 310 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase COP1; Ultraviolet-B receptor UVR8
- EC
- 2.3.2.27
- UniProt
- P43254, Q9FN03
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase COP1 (EC 2.3.2.27) | protein | 304 | 2% helix, 51% strand | P43254 |
| B | Ultraviolet-B receptor UVR8 | protein | 6 | 0% helix, 17% strand | Q9FN03 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 308 | 0.75 | 0.87 | 50 | empty |
| 2 | 88 | 0.46 | 0.81 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 473 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation).
Compared structures
- 6QTQ · Crystal structure of an Arabidopsis WD40 domain in complex with photoreceptor · the same entry in another collection · chain A against A, TM-score 1.00
- P43254 · AlphaFold monomer V2.0 prediction for E3 ubiquitin-protein ligase COP1 (P43254) · a predicted model of the same protein · chain A against A, TM-score 1.00
- Q9FN03 · AlphaFold monomer V2.0 prediction for ultraviolet-B receptor UVR8 (Q9FN03) · a predicted model of the same protein · chain B against A, TM-score 0.58
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 P43254
- Every structure of UniProt Q9FN03
- Elsewhere: RCSB PDB 6QTQ · PDBe 6QTQ · UniProt P43254 · UniProt Q9FN03
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