5KWN: E3 ubiquitin-protein ligase COP1

The WD domain ofArabidopsis thaliana E3 Ubiquitin Ligase COP1 in complex with peptide from HY5. Determined by X-ray diffraction at 1.42 Å resolution. Released 26 Jul 2017.

Method: X-ray diffraction
Resolution: 1.42 Å
Organisms: Arabidopsis thaliana, Arabidopsis
Chains: 2
Atoms: 2,877
Mol. weight: 40.26 kDa
Released: 26 Jul 2017

Explore 5KWN in 3D Show helices and sheets RCSB PDB PDBe

Secondary structure: helices and β-sheets

5KWN contains 3 α-helices and 30 β-strands across 2 chains. Residue ranges use author residue numbering, as in the PDB file, from PDBe. To see them in 3D, choose the Cartoon representation with Secondary structure coloring: helices, sheets and coils get different colors.

Chain A: 2 helices, 29 β-strands

Element	Residues	Length	Sheet
β-strand	355-362	8	1
β-strand	374-379	6	2
β-strand	385-390	6	2
β-strand	394-399	6	2
α-helix	400-405	6
α-helix	408-410	3
β-strand	415-418	4	2
β-strand	423-428	6	3
β-strand	435-440	6	3
β-strand	445-449	5	3
β-strand	454-459	6	3
β-strand	466-471	6	4
β-strand	478-483	6	4
β-strand	487-492	6	4
β-strand	500-503	4	4
β-strand	508-513	6	5
β-strand	520-525	6	5
β-strand	530-534	5	5
β-strand	543-545	3	5
β-strand	552-557	6	6
β-strand	562-567	6	6
β-strand	571-576	6	6
β-strand	581-587	7	6
β-strand	594	1	7
β-strand	598-600	3	8
β-strand	604-607	4	8
β-strand	613-618	6	8
β-strand	626-629	4	8
β-strand	647-652	6	1
β-strand	658-663	6	1
β-strand	668-674	7	1

Chain U: 1 helix, 1 β-strand

Element	Residues	Length	Sheet
β-strand	357	1	7
α-helix	358-360	3

Molecules and chains

Molecule	Chains	Type	Length	Organism	UniProt
E3 ubiquitin-protein ligase COP1	A	protein	336	Arabidopsis thaliana	P43254 (AlphaFold model)
peptide 16-mer	U	protein	19	Arabidopsis	O24646 (AlphaFold model)

Sequence of entity 1 (A), FASTA

>5KWN_1 E3 ubiquitin-protein ligase COP1 (chains A)
MHHHHHHHHTFTRYSRLRVIAEIRHGDIFHSANIVSSIEFDRDDELFATAGVSRCIKVFD
FSSVVNEPADMQCPIVEMSTRSKLSCLSWNKHEKNHIASSDYEGIVTVWDVTTRQSLMEY
EEHEKRAWSVDFSRTEPSMLVSGSDDCKVKVWCTRQEASVINIDMKANICCVKYNPGSSN
YIAVGSADHHIHYYDLRNISQPLHVFSGHKKAVSYVKFLSNNELASASTDSTLRLWDVKD
NLPVRTFRGHTNEKNFVGLTVNSEYLACGSETNEVYVYHKEITRPVTSHRFGSPDMDDAE
EEAGSYFISAVCWKSDSPTMLTANSQGTIKVLVLAA

Sequence of entity 2 (U), FASTA

>5KWN_2 peptide 16-mer (chains U)
IESDEEIRRVPEFGGEAVG

Primary citation

The COP1 WD domain in complex with HY5 peptide. Uljon, S., Blacklow, S. To be published.

Other PDB entries of the same protein (UniProt P43254 (AlphaFold model), which also has an AlphaFold model), best resolution first:

6QTS 1.11 Å, Crystal structure of a mutant Arabidopsis WD40 domain in complex with a photoreceptor
6QTO 1.27 Å, Crystal structure of an Arabidopsis WD40 domain in complex with a transcription factor
6QTQ 1.3 Å, Crystal structure of an Arabidopsis WD40 domain in complex with photoreceptor
6QTU 1.3 Å, Crystal structure of Arabidopsis WD40 domain in complex with a BBX transcription factor
6QTV 1.31 Å, Crystal structure of an Arabidopsis WD40 domain in complex with an atypical bHLH…
6QTR 1.37 Å, Crystal structure of a mutant Arabidopsis WD40 domain in complex with a transcription…
6QTW 1.39 Å, Crystal structure of an Arabidopsis WD40 domain in complex with a blue light photoreceptor
6QTT 1.51 Å, Crystal structure of an Arabidopsis WD40 domain in complex with a transcription factor…
5IGO 1.6 Å, WD40 domain of Arabidopsis thaliana E3 Ubiquitin Ligase COP1 in complex with peptide…
6QTX 1.95 Å, Crystal structure of an Arabidopsis WD40 domain in complex with a flowering…
7VGG 3.1 Å, Cryo-EM structure of Ultraviolet-B activated UVR8 in complex with COP1

Browse structure collections

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