MolNFT v1 · #161943 · protein
Crystal structure of an arabidopsis WD40 domain in complex with an atypical bhlh transcription factor
6QTV · E3 ubiquitin-protein ligase COP1: “Crystal structure of an arabidopsis WD40 domain in complex with an atypical bhlh transcription factor”. X-ray diffraction, 2 pockets (best druggability 0.79). MolNFT v1 #161943 on GenesisL1: 3D…
- 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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