Research workbench
Crystal structure of an arabidopsis WD40 domain in complex with an atypical bhlh transcription factor
Analyse Crystal structure of an arabidopsis WD40 domain in complex with an atypical… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6QTV
- Type
- protein
- Length
- 313 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase COP1; Transcription factor HFR1
- EC
- 2.3.2.27
- UniProt
- P43254, Q9FE22
- Pockets
- 2 · best druggability 0.79
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 | 305 | 2% helix, 51% strand | P43254 |
| B | Transcription factor HFR1 | protein | 8 | 0% helix, 13% strand | Q9FE22 |
Ligands and binding sites
- MLI · Malonate ion · additive · 3 copies · chains A
- GOL · Glycerol · additive · 2 copies · chains A, B
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 | 361 | 0.79 | 0.89 | 52 | GOL |
| 2 | 50 | 0.34 | 0.79 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 604 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 1 modified (oxidation).
Compared structures
- 6QTV · Crystal structure of an Arabidopsis WD40 domain in complex with an atypical bHLH… · 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
- Q9FE22 · AlphaFold monomer V2.0 prediction for transcription factor HFR1 (Q9FE22) · a predicted model of the same protein · chain B against A, TM-score 0.45
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 Q9FE22
- Elsewhere: RCSB PDB 6QTV · PDBe 6QTV · UniProt P43254 · UniProt Q9FE22
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