5FQD	Ligase	date	Dec 09, 2015
title	Structural Basis Of Lenalidomide Induced Ck1a Degradation By Crl4crbn Ubiquitin Ligase
authors	G.Petzold, E.S.Fischer, N.H.Thoma
compound		source
Molecule: Dna Damage-Binding Protein 1 Chain: A, D Synonym: Ddb P127 Subunit, Dna Damage-Binding Protein A, Dd -Specific Dna-Binding Protein 1, Hbv X-Associated Protein 1 Uv-Damaged Dna-Binding Factor, Uv-Damaged Dna-Binding Prote Ddb 1, Xpe-Binding Factor, Xpe-Bf, Xeroderma Pigmentosum Gr Complementing Protein, Xpce; Ec: 6.3.2.19 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Trichoplusia Ni Expression_system_common: Cabbage Looper Expression_system_taxid: 7111 Expression_system_cell_line: High Five Expression_system_vector_type: Baculovirus
Molecule: Protein Cereblon Chain: B, E Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Trichoplusia Ni Expression_system_common: Cabbage Looper Expression_system_taxid: 7111 Expression_system_cell_line: High Five Expression_system_vector_type: Baculovirus
Molecule: Casein Kinase I Isoform Alpha Chain: C, F Synonym: Cki-Alpha, Ck1, Caseine Kinase 1a Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Expression_system: Trichoplusia Ni Expression_system_common: Cabbage Looper Expression_system_taxid: 7111 Expression_system_cell_line: High Five Expression_system_vector_type: Baculovirus
symmetry	Space Group: P 1	R_factor 0.181 R_Free 0.210
crystal cell	length a length b length c angle alpha angle beta angle gamma 87.970 109.930 112.400 106.02 93.19 101.63
method	X-Ray Diffraction	resolution	2.45 Å
ligand	LVY, ZN	enzyme	Ligase E.C.6.3.2.19 BRENDA
Gene Ontology	Chain Function Process Component A, D E, B F, C
Primary reference	Structural basis of lenalidomide-induced CK1alpha degradation by the CRL4 ubiquitin ligase., Petzold G, Fischer ES, Thoma NH, Nature. 2016 Feb 24. doi: 10.1038/nature16979. PMID:26909574

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (993 Kb) [Save to disk] Biological Unit Coordinates (5fqd.pdb1.gz) 497 Kb Biological Unit Coordinates (5fqd.pdb2.gz) 495 Kb LPC: Ligand-Protein Contacts for 5FQD CSU: Contacts of Structural Units for 5FQD Structure Factors (7715 Kb) Retrieve 5FQD in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5FQD from S2C, [Save to disk] Re-refined 5fqd structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

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Proteopedia, because life has more than 2D. On Jmol, a nice Rasmol like molecule viewer. This is good for easiest viewing of basic structure. On FirstGlance, an excellent tool for a guided tour on the structure components, by E. Martz.

Visual 3D analysis of 5FQD

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Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5fqd_C] [5fqd_A] [5fqd_D] [5fqd_E] [5fqd_F] [5fqd_B] [5fqd] SWISS-PROT database: Domain organization of by SWISSPFAM Domains found in 5FQD: [LON] [STYKc ] by SMART

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