6H0G Signaling Protein date Jul 09, 2018
title Structure Of The Ddb1-Crbn-Pomalidomide Complex Bound To Znf
authors R.D.Bunker, G.Petzold, N.H.Thoma
compound source
Molecule: Dna Damage-Binding Protein 1,Dna Damage-Binding P Dna Damage-Binding Protein 1,Ddb1 (Dna Damage Binding Prote Damage-Binding Protein 1,Dna Damage-Binding Protein 1,Dna D Binding Protein 1;
Chain: A, D
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,Ddb P127 Subunit,Dna Damage-Binding Protein A, Damage-Specific Dna-Binding Protein 1,Hbv X-Associated Prot 1,Uv-Damaged Dna-Binding Factor,Uv-Damaged Dna-Binding Prot Ddb 1,Xpe-Binding Factor,Xpe-Bf,Xeroderma Pigmentosum Group Complementing Protein,Xpce;
Engineered: Yes
Mutation: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Ddb1, Xap1
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111

Molecule: Protein Cereblon
Chain: B, E
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: Zinc Finger Protein 692
Chain: C, F
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Znf692
Expression_system: Trichoplusia Ni
Expression_system_common: Cabbage Looper
Expression_system_taxid: 7111
symmetry Space Group: P 1 21 1
R_factor 0.221 R_Free 0.256
crystal
cell
length a length b length c angle alpha angle beta angle gamma
112.510 99.530 166.940 90.00 108.49 90.00
method X-Ray Diffractionresolution 4.25 Å
Gene
Ontology
ChainFunctionProcessComponent
A, D


E, B


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] (1751 Kb) [Save to disk]
  • Biological Unit Coordinates (6h0g.pdb1.gz) 871 Kb
  • Biological Unit Coordinates (6h0g.pdb2.gz) 875 Kb
  • CSU: Contacts of Structural Units for 6H0G
  • Structure Factors (903 Kb)
  • Retrieve 6H0G in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 6H0G from S2C, [Save to disk]
  • View 6H0G 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 6H0G
  • 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 6h0g from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [6h0g_E] [6h0g_A] [6h0g_B] [6h0g_D] [6h0g_C] [6h0g_F]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 6H0G
  • Community annotation for 6H0G at PDBWiki (http://pdbwiki.org)

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