7BQV Metal Binding Protein date Mar 25, 2020
title Cereblon In Complex With Sall4 And (S)-5-Hydroxythalidomide
authors H.Furihata, Y.Miyauchi, A.Asano, M.Tanokura, T.Miyakawa
compound source
Molecule: Protein Cereblon
Chain: A
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Crbn, Ad-006
Expression_system: Escherichia Coli
Expression_system_taxid: 562

Molecule: Sal-Like Protein 4
Chain: B
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: C 2 2 21
R_factor 0.197 R_Free 0.223
crystal
cell
length a length b length c angle alpha angle beta angle gamma
83.621 93.895 43.682 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand F4U, SO4, ZN enzyme
Primary referenceStructural bases of IMiD selectivity that emerges by 5-hydroxythalidomide., Furihata H, Yamanaka S, Honda T, Miyauchi Y, Asano A, Shibata N, Tanokura M, Sawasaki T, Miyakawa T, Nat Commun. 2020 Sep 14;11(1):4578. doi: 10.1038/s41467-020-18488-4. PMID:32929090
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (52 Kb) [Save to disk]
  • Biological Unit Coordinates (7bqv.pdb1.gz) 47 Kb
  • LPC: Ligand-Protein Contacts for 7BQV
  • CSU: Contacts of Structural Units for 7BQV
  • Structure Factors (427 Kb)
  • Retrieve 7BQV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 7BQV from S2C, [Save to disk]
  • View 7BQV 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 7BQV
  • 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 7bqv from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [7bqv_A] [7bqv_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 7BQV
  • Community annotation for 7BQV at PDBWiki (http://pdbwiki.org)

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