6H0F Signaling Protein date Jul 09, 2018
title Structure Of Ddb1-Crbn-Pomalidomide Complex Bound To Ikzf1(Z
authors G.Petzold, R.D.Bunker, N.H.Thoma
compound source
Molecule: Dna Damage-Binding Protein 1,Dna Damage-Binding P Dna Damage-Binding Protein 1,Dna Damage-Binding Protein 1;
Chain: A, D, G, J
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddb1, Xap1
Expression_system: Trichoplusia Ni Cypovirus 15
Expression_system_taxid: 134606

Molecule: Protein Cereblon
Chain: B, E, H, K
Engineered: Yes
Mutation: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Crbn, Ad-006
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Dna-Binding Protein Ikaros
Chain: C, F, I, L
Synonym: Ikaros Family Zinc Finger Protein 1,Lymphoid Trans Factor Lyf-1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ikzf1, Ik1, Ikaros, Lyf1, Znfn1a1
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
symmetry Space Group: P 21 21 21
R_factor 0.212 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
161.450 177.860 242.470 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.25 Å
Gene
Ontology
ChainFunctionProcessComponent
A, J, D, G


F, C, I, L


K, E, B, H


Primary referenceDefining the human C2H2 zinc finger degrome targeted by thalidomide analogs through CRBN., Sievers QL, Petzold G, Bunker RD, Renneville A, Slabicki M, Liddicoat BJ, Abdulrahman W, Mikkelsen T, Ebert BL, Thoma NH, Science. 2018 Nov 2;362(6414). pii: 362/6414/eaat0572. doi:, 10.1126/science.aat0572. PMID:30385546
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (3290 Kb) [Save to disk]
  • Biological Unit Coordinates (6h0f.pdb1.gz) 821 Kb
  • Biological Unit Coordinates (6h0f.pdb2.gz) 827 Kb
  • Biological Unit Coordinates (6h0f.pdb3.gz) 832 Kb
  • Biological Unit Coordinates (6h0f.pdb4.gz) 835 Kb
  • CSU: Contacts of Structural Units for 6H0F
  • Structure Factors (7445 Kb)
  • Retrieve 6H0F in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6H0F from S2C, [Save to disk]
  • View 6H0F 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 6H0F
  • 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 6h0f from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6h0f_K] [6h0f_L] [6h0f_A] [6h0f_B] [6h0f_J] [6h0f_C] [6h0f_E] [6h0f_I] [6h0f_G] [6h0f_F] [6h0f_D] [6h0f_H]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6H0F
  • Community annotation for 6H0F 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
    Bioinformatics Unit
    Weizmann Institute of Science