6UML Ligase date Oct 09, 2019
title Structural Basis For Thalidomide Teratogenicity Revealed By Cereblon-Ddb1-Sall4-Pomalidomide Complex
authors T.L.Clayton, M.E.Matyskiela, B.E.Pagarigan, E.T.Tran, P.P.Chambe
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_taxid: 7108

Molecule: Protein Cereblon
Chain: 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

Molecule: Sal-Like Protein 4
Chain: E
Synonym: Zinc Finger Protein 797,Zinc Finger Protein Sall4
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sall4, Znf797
Expression_system: Escherichia Coli
Expression_system_taxid: 562
symmetry Space Group: P 1 21 1
R_factor 0.204 R_Free 0.267
crystal
cell
length a length b length c angle alpha angle beta angle gamma
77.409 127.725 110.174 90.00 109.69 90.00
method X-Ray Diffractionresolution 3.58 Å
ligand Y70, ZN enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


C


Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (460 Kb) [Save to disk]
  • Biological Unit Coordinates (6uml.pdb1.gz) 452 Kb
  • LPC: Ligand-Protein Contacts for 6UML
  • CSU: Contacts of Structural Units for 6UML
  • Structure Factors (874 Kb)
  • Retrieve 6UML in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6UML from S2C, [Save to disk]
  • View 6UML 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 6UML
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • Fold representative 6uml from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6uml_C] [6uml_E] [6uml_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6UML
  • Community annotation for 6UML at PDBWiki (http://pdbwiki.org)

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