5V3O	Ligase	date	Mar 07, 2017
title	Cereblon In Complex With Ddb1 And Cc-220
authors	M.Matyskiela, B.Pagarigan, P.Chamberlain
compound		source
Molecule: Dna Damage-Binding Protein 1 Chain: A 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_common: Fall Armyworm Expression_system_taxid: 7108
Molecule: Protein Cereblon Chain: C Fragment: Residues 40-442 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Crbn, Ad-006 Expression_system: Spodoptera Frugiperda Expression_system_common: Fall Armyworm Expression_system_taxid: 7108
symmetry	Space Group: P 21 21 21	R_factor 0.204 R_Free 0.267
crystal cell	length a length b length c angle alpha angle beta angle gamma 111.029 126.886 172.487 90.00 90.00 90.00
method	X-Ray Diffraction	resolution	3.20 Å
ligand	8W7, ZN	enzyme
Gene Ontology	Chain Function Process Component A C
Primary reference	A Cereblon Modulator (CC-220) with Improved Degradation of Ikaros and Aiolos., Matyskiela ME, Zhang W, Man HW, Muller G, Khambatta G, Baculi F, Hickman M, LeBrun L, Pagarigan B, Carmel G, Lu CC, Lu G, Riley M, Satoh Y, Schafer P, Daniel TO, Carmichael J, Cathers BE, Chamberlain PP, J Med Chem. 2017 Apr 20. doi: 10.1021/acs.jmedchem.6b01921. PMID:28425720

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (472 Kb) [Save to disk] Biological Unit Coordinates (5v3o.pdb1.gz) 464 Kb LPC: Ligand-Protein Contacts for 5V3O CSU: Contacts of Structural Units for 5V3O Structure Factors (1189 Kb) Retrieve 5V3O in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5V3O from S2C, [Save to disk] Re-refined 5v3o structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5V3O 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 5V3O

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: [5v3o_A] [5v3o_C] [5v3o] SWISS-PROT database: Domain organization of by SWISSPFAM

Other resources with information on 5V3O

Community annotation for 5V3O at PDBWiki (http://pdbwiki.org)

You may enter another PDB ID code

Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]

---

OCA© by Jaime Prilusky, 1996-2014,2022 Bioinformatics Unit Weizmann Institute of Science

---