5T35	Ligase	date	Aug 24, 2016
title	The Protac Mz1 In Complex With The Second Bromodomain Of Brd Pvhl:Elonginc:Elonginb
authors	M.S.Gadd, M.Zengerle, A.Ciulli
compound		source
Molecule: Bromodomain-Containing Protein 4 Chain: A, E Synonym: Protein Hunk1 Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Brd4, Hunk1 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pnic28
Molecule: Transcription Elongation Factor B Polypeptide 2 Chain: B, F Synonym: Elongin 18 Kda Subunit,Elongin-B,Elob,Rna Polymera Transcription Factor Siii Subunit B,Siii P18; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Tceb2 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pcdfduet-1
Molecule: Transcription Elongation Factor B Polypeptide 1 Chain: C, G Synonym: Elongin 15 Kda Subunit,Elongin-C,Eloc,Rna Polymera Transcription Factor Siii Subunit C,Siii P15; Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Tceb1 Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_vector_type: Plasmid Expression_system_plasmid: Pcdfduet-1
Molecule: Von Hippel-Lindau Disease Tumor Suppressor Chain: D, H Synonym: Protein G7,Pvhl Engineered: Yes		Organism_scientific: Homo Sapiens Organism_common: Human Organism_taxid: 9606 Gene: Vhl Expression_system: Escherichia Coli Bl21(De3) Expression_system_taxid: 469008 Expression_system_vector_type: Plasmid Expression_system_plasmid: Phat4
symmetry	Space Group: P 32	R_factor 0.206 R_Free 0.231
crystal cell	length a length b length c angle alpha angle beta angle gamma 102.306 102.306 144.329 90.00 90.00 120.00
method	X-Ray Diffraction	resolution	2.70 Å
ligand	759	enzyme
Gene Ontology	Chain Function Process Component C, G F, B
Primary reference	Structural basis of PROTAC cooperative recognition for selective protein degradation., Gadd MS, Testa A, Lucas X, Chan KH, Chen W, Lamont DJ, Zengerle M, Ciulli A, Nat Chem Biol. 2017 Mar 13. doi: 10.1038/nchembio.2329. PMID:28288108

Data retrieval

Asymmetric unit, PDB entry: [header only] [complete with coordinates] (307 Kb) [Save to disk] Biological Unit Coordinates (5t35.pdb1.gz) 150 Kb Biological Unit Coordinates (5t35.pdb2.gz) 153 Kb LPC: Ligand-Protein Contacts for 5T35 CSU: Contacts of Structural Units for 5T35 Structure Factors (969 Kb) Retrieve 5T35 in mmCIF format [Save to disk] SEQRES to COORDINATES correlation for 5T35 from S2C, [Save to disk] Re-refined 5t35 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models

View 5T35 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 5T35

Ramachandran plot from PDBSum

Structure-derived information

Electron Density related parameters from EDS Electron Density Server, at Upsala Dipole moment, from Dipole Server at Weizmann Institute

Sequence-derived information

View one-letter amino acid or nucleotide sequence for each chain: [5t35_A] [5t35_E] [5t35_C] [5t35_F] [5t35_H] [5t35_D] [5t35] [5t35_B] [5t35_G] SWISS-PROT database: Domain organization of by SWISSPFAM

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