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RCSB PDB - 1LVB: CATALYTICALLY INACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH SUBSTRATE

 1LVB | pdb_00001lvb

CATALYTICALLY INACTIVE TOBACCO ETCH VIRUS PROTEASE COMPLEXED WITH SUBSTRATE


Experimental Data Snapshot

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.20 Å
  • R-Value Free:&nbsp
    0.263 (Depositor), 0.270 (DCC)&nbsp
  • R-Value Work:&nbsp
    0.236 (Depositor), 0.250 (DCC)&nbsp

wwPDB Validation&nbsp &nbsp3D Report&nbspFull Report


This is version 1.4 of the entry. See complete&nbsphistory.&nbsp


Literature

Structural basis for the substrate specificity of tobacco etch virus protease.

Phan, J.,&nbspZdanov, A.,&nbspEvdokimov, A.G.,&nbspTropea, J.E.,&nbspPeters III, H.K.,&nbspKapust, R.B.,&nbspLi, M.,&nbspWlodawer, A.,&nbspWaugh, D.S.

(2002) J Biological Chem&nbsp277: 50564-50572

  • DOI:&nbsphttps://doi.org/10.1074/jbc.M207224200
  • Primary Citation of Related Structures: &nbsp
    1LVB, 1LVM

  • PubMed Abstract:&nbsp

    Because of its stringent sequence specificity, the 3C-type protease from tobacco etch virus (TEV) is frequently used to remove affinity tags from recombinant proteins. It is unclear, however, exactly how TEV protease recognizes its substrates with such high selectivity. The crystal structures of two TEV protease mutants, inactive C151A and autolysis-resistant S219D, have now been solved at 2.2- and 1.8-A resolution as complexes with a substrate and product peptide, respectively. The enzyme does not appear to have been perturbed by the mutations in either structure, and the modes of binding of the product and substrate are virtually identical. Analysis of the protein-ligand interactions helps to delineate the structural determinants of substrate specificity and provides guidance for reengineering the enzyme to further improve its utility for biotechnological applications.


  • Organizational Affiliation:&nbsp
    • Macromolecular Crystallography Laboratory, Center for Cancer Research, NCI-Frederick, National Institutes of Health, Frederick, Maryland 21702-1201, USA.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
CATALYTIC DOMAIN OF THE NUCLEAR INCLUSION PROTEIN A (NIA)A,
C [auth B]
243Tobacco etch virusMutation(s): 7&nbsp
UniProt
Find proteins for&nbspP04517&nbsp(Tobacco etch virus)
Explore&nbspP04517&nbsp
Go to UniProtKB: &nbspP04517
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04517
Sequence Annotations
Expand
  • Reference Sequence

Find similar proteins by:  Sequence   |   3D Structure  

Entity ID: 2
MoleculeChains Sequence LengthOrganismDetailsImage
OLIGOPEPTIDE SUBSTRATE FOR THE PROTEASEB [auth C],
D
10Tobacco etch virusMutation(s): 0&nbsp
UniProt
Find proteins for&nbspP04517&nbsp(Tobacco etch virus)
Explore&nbspP04517&nbsp
Go to UniProtKB: &nbspP04517
Entity Groups &nbsp
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP04517
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A,
C [auth B]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET
Experimental Data & Validation

Experimental Data

  • Method:&nbspX-RAY DIFFRACTION
  • Resolution:&nbsp2.20 Å
  • R-Value Free:&nbsp 0.263 (Depositor), 0.270 (DCC)&nbsp
  • R-Value Work:&nbsp 0.236 (Depositor), 0.250 (DCC)&nbsp
Space Group:&nbspP 42 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 125.317α = 90
b = 125.317β = 90
c = 127.933γ = 90
Software Package:
Software NamePurpose
HKL-2000data collection
SCALEPACKdata scaling
SOLVEphasing
CNSrefinement
HKL-2000data reduction

Structure Validation

View&nbspFull Validation Report



Entry History&nbsp

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2002-11-27
    Type: Initial release
  • Version 1.1: 2008-04-28
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2021-10-27
    Changes: Database references, Derived calculations
  • Version 1.4: 2024-11-06
    Changes: Data collection, Structure summary