5NVV Ligase date May 04, 2017
title Pvhl:Elob:Eloc In Complex With (2s,4r)-4-Hydroxy-1-((S)-2-(2 Hydroxyacetamido)-3,3-Dimethylbutanoyl)-N-(4-(4-Methylthiaz Benzyl)Pyrrolidine-2-Carboxamide (Ligand 3)
authors M.S.Gadd, P.Soares, C.Galdeano, A.Ciulli
compound source
Molecule: Elongin-B
Chain: A, D, G, J
Synonym: Elob,Elongin 18 Kda Subunit,Rna Polymerase II Tran Factor Siii Subunit B,Siii P18,Transcription Elongation Fac Polypeptide 2;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Elob, Tceb2
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdfduet-1

Molecule: Elongin-C
Chain: B, E, H, K
Synonym: Eloc,Elongin 15 Kda Subunit,Rna Polymerase II Tran Factor Siii Subunit C,Siii P15,Transcription Elongation Fac Polypeptide 1;
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Eloc, Tceb1
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pcdfduet-1

Molecule: Von Hippel-Lindau Disease Tumor Suppressor
Chain: C, F, I, L
Synonym: Protein G7,Pvhl
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Vhl
Expression_system: Escherichia Coli
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Phat4
symmetry Space Group: P 41 2 2
R_factor 0.203 R_Free 0.245
crystal
cell
length a length b length c angle alpha angle beta angle gamma
93.299 93.299 364.958 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
ligand 9BT, CAS enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, J, D, G


H, K, E, B


Primary referenceGroup-Based Optimization of Potent and Cell-Active Inhibitors of the von Hippel-Lindau (VHL) E3 Ubiquitin Ligase: Structure-Activity Relationships Leading to the Chemical Probe (2S,4R)-1-((S)-2-(1-Cyanocyclopropanecarboxamido)-3,3-dimethylbutanoyl)-4-hydroxy -N-(4-(4-methylthiazol-5-yl)benzyl)pyrrolidine-2-carboxamide (VH298)., Soares P, Gadd MS, Frost J, Galdeano C, Ellis L, Epemolu O, Rocha S, Read KD, Ciulli A, J Med Chem. 2017 Sep 18. doi: 10.1021/acs.jmedchem.7b00675. PMID:28853884
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (461 Kb) [Save to disk]
  • Biological Unit Coordinates (5nvv.pdb1.gz) 117 Kb
  • Biological Unit Coordinates (5nvv.pdb2.gz) 117 Kb
  • Biological Unit Coordinates (5nvv.pdb3.gz) 117 Kb
  • Biological Unit Coordinates (5nvv.pdb4.gz) 118 Kb
  • LPC: Ligand-Protein Contacts for 5NVV
  • CSU: Contacts of Structural Units for 5NVV
  • Structure Factors (2772 Kb)
  • Retrieve 5NVV in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5NVV from S2C, [Save to disk]
  • View 5NVV 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 5NVV
  • 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: [5nvv_B] [5nvv_E] [5nvv_H] [5nvv_D] [5nvv_I] [5nvv_C] [5nvv_G] [5nvv_F] [5nvv_K] [5nvv_J] [5nvv_L] [5nvv_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5NVV
  • Community annotation for 5NVV at PDBWiki (http://pdbwiki.org)

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