5HXB	Ligase	date	Jan 30, 2016
title	Cereblon In Complex With Ddb1, Cc-885, And Gspt1
authors	P.P.Chamberlain, M.Matyskiela, B.Pagarigan
compound		source
Molecule: Eukaryotic Peptide Chain Release Factor Gtp-Bindi Erf3a; Chain: X, A Synonym: Erf3a,G1 To S Phase Transition Protein 1 Homolog Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Gspt1, Erf3a Expression_system: Escherichia Coli Expression_system_taxid: 562
Molecule: Dna Damage-Binding Protein 1 Chain: Y, B Synonym: Ddb P127 Subunit,Dna Damage-Binding Protein A,Ddba Specific Dna-Binding Protein 1,Hbv X-Associated Protein 1,X Damaged Dna-Binding Factor,Uv-Damaged Dna-Binding Protein 1 Xpe-Binding Factor,Xpe-Bf,Xeroderma Pigmentosum Group E-Com Protein,Xpce; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Ddb1, Xap1 Expression_system: Spodoptera Frugiperda Expression_system_taxid: 7108
Molecule: Protein Cereblon Chain: Z, C Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Crbn, Ad-006 Expression_system: Spodoptera Frugiperda Expression_system_taxid: 7108
symmetry	Space Group: P 1 2 1	R_factor 0.224 R_Free 0.273
crystal cell	length a length b length c angle alpha angle beta angle gamma 156.747 111.522 175.057 90.00 95.81 90.00
method	X-Ray Diffraction	resolution	3.60 Å
ligand	85C, ZN	enzyme
Gene Ontology	Chain Function Process Component A, X Y, B Z, C
Primary reference	A novel cereblon modulator recruits GSPT1 to the CRL4CRBN ubiquitin ligase., Matyskiela ME, Lu G, Ito T, Pagarigan B, Lu CC, Miller K, Fang W, Wang NY, Nguyen D, Houston J, Carmel G, Tran T, Riley M, Nosaka L, Lander GC, Gaidarova S, Xu S, Ruchelman AL, Handa H, Carmichael J, Daniel TO, Cathers BE, Lopez-Girona A, Chamberlain PP, Nature. 2016 Jun 22. doi: 10.1038/nature18611. PMID:27338790

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (981 Kb) [Save to disk] Biological Unit Coordinates (5hxb.pdb1.gz) 492 Kb Biological Unit Coordinates (5hxb.pdb2.gz) 485 Kb LPC: Ligand-Protein Contacts for 5HXB CSU: Contacts of Structural Units for 5HXB Structure Factors (1470 Kb) Retrieve 5HXB in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5HXB from S2C, [Save to disk] Re-refined 5hxb structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5HXB in 3D

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 5HXB

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5hxb_C] [5hxb_Z] [5hxb_A] [5hxb_Y] [5hxb_B] [5hxb_X] [5hxb] SWISS-PROT database: Domain organization of by SWISSPFAM Domain found in 5HXB: [LON ] by SMART

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