MolNFT v1 · #161939 · protein
Crystal structure of a mutant arabidopsis WD40 domain in complex with a transcription factor
6QTR · E3 ubiquitin-protein ligase COP1: “Crystal structure of a mutant arabidopsis WD40 domain in complex with a transcription factor”. X-ray diffraction, 1 ligand (SO4), 2 pockets (best druggability 0.75). MolNFT v1 #161939 on GenesisL1…
- PDB
- 6QTR
- Type
- protein
- Length
- 318 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- E3 ubiquitin-protein ligase COP1; Transcription factor HY5
- EC
- 2.3.2.27
- UniProt
- P43254, O24646
- Ligands
- SO4
- Pockets
- 2 · best druggability 0.75
Structure
x-ray diffraction · 2 distinct chains · 3% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | E3 ubiquitin-protein ligase COP1 (EC 2.3.2.27) | protein | 307 | 3% helix, 50% strand | P43254 |
| B | Transcription factor HY5 | protein | 11 | 0% helix, 9% strand | O24646 |
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 | 314 | 0.75 | 0.87 | 47 | SO4 |
| 2 | 59 | 0.36 | 0.78 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 686 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 modified (oxidation, artifact).
Compared structures
- 6QTR · Crystal structure of a mutant Arabidopsis WD40 domain in complex with a transcription… · 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
- O24646 · AlphaFold monomer V2.0 prediction for transcription factor HY5 (O24646) · a predicted model of the same protein · chain B against A, TM-score 0.33
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 O24646
- Elsewhere: RCSB PDB 6QTR · PDBe 6QTR · UniProt P43254 · UniProt O24646
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