Research workbench
Crystal structure of arabidopsis WD40 domain in complex with a bbx transcription factor
Analyse Crystal structure of arabidopsis WD40 domain in complex with a bbx… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QTU
- Type
- protein
- Length
- 314 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase COP1; B-box zinc finger protein 24
- EC
- 2.3.2.27
- UniProt
- P43254, Q96288
- Pockets
- 2 · best druggability 0.77
Structure
x-ray diffraction · 2 distinct chains · 2% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase COP1 (EC 2.3.2.27) | protein | 307 | 2% helix, 50% strand | P43254 |
| B | B-box zinc finger protein 24 | protein | 7 | 0% helix, 14% strand | Q96288 |
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 | 350 | 0.77 | 0.88 | 51 | empty |
| 2 | 53 | 0.33 | 0.78 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 566 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6QTU · Crystal structure of Arabidopsis WD40 domain in complex with a BBX transcription factor · 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 0.99
- Q96288 · AlphaFold monomer V2.0 prediction for B-box zinc finger protein 24 (Q96288) · a predicted model of the same protein · chain B against A, TM-score 0.49
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 Q96288
- Elsewhere: RCSB PDB 6QTU · PDBe 6QTU · UniProt P43254 · UniProt Q96288
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