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 Diffraction	resolution	4.25 Å
ligand	Y70, ZN	enzyme
Gene Ontology	Chain Function Process Component A, D E, B
Primary reference	Defining 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] (1712 Kb) [Save to disk] Biological Unit Coordinates (6h0g.pdb1.gz) 852 Kb Biological Unit Coordinates (6h0g.pdb2.gz) 856 Kb LPC: Ligand-Protein Contacts for 6H0G 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

Ramachandran plot from PDBSum

Structure-derived information

Dipole moment, from Dipole Server at Weizmann Institute

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

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