1LVM Viral Protein date May 28, 2002
title Catalytically Active Tobacco Etch Virus Protease Complexed W Product
authors J.Phan, A.Zdanov, A.G.Evdokimov, J.E.Tropea, H.K.Peters Iii, R.B. M.Li, A.Wlodawer, D.S.Waugh
compound source
Molecule: Catalytic Domain Of The Nuclear Inclusion Protein
Chain: A, B
Fragment: Residues 1-221
Engineered: Yes
Mutation: Yes
Organism_scientific: Tobacco Etch Virus
Organism_taxid: 12227
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Prk529
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Bl21(De3)

Molecule: Oligopeptide Substrate For The Protease
Chain: C, D
Fragment: Residues 302-310
Engineered: Yes

Organism_scientific: Tobacco Etch Virus
Organism_taxid: 12227
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Prk529
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Bl21(De3)

Molecule: Catalytic Domain Of The Nuclear Inclusion Protein
Chain: E
Fragment: Residues 230-236
Engineered: Yes

Organism_scientific: Tobacco Etch Virus
Organism_taxid: 12227
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Prk529
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Bl21(De3)
symmetry Space Group: P 43 21 2
R_factor 0.171 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
75.505 75.505 183.167 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand ACE enzyme
related structures by homologous chain: 1LVB
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceStructural basis for the substrate specificity of tobacco etch virus protease., Phan J, Zdanov A, Evdokimov AG, Tropea JE, Peters HK 3rd, Kapust RB, Li M, Wlodawer A, Waugh DS, J Biol Chem 2002 Dec 27;277(52):50564-72. Epub 2002 Oct 10. PMID:12377789
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (94 Kb) [Save to disk]
  • Biological Unit Coordinates (1lvm.pdb1.gz) 47 Kb
  • Biological Unit Coordinates (1lvm.pdb2.gz) 42 Kb
  • Biological Unit Coordinates (1lvm.pdb3.gz) 87 Kb
  • LPC: Ligand-Protein Contacts for 1LVM
  • CSU: Contacts of Structural Units for 1LVM
  • Likely Quarternary Molecular Structure file(s) for 1LVM
  • Structure Factors (619 Kb)
  • Retrieve 1LVM in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1LVM from S2C, [Save to disk]
  • Re-refined 1lvm structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1LVM 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 1LVM
  • 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
  • 3D motif for 1LVM, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1lvm.1, region A:,E [Jmol] [rasmolscript] [script source]
        - Domain d1lvmb_, region B [Jmol] [rasmolscript] [script source]
  • Class (fold), Architecture (subfold), Topology, Homologous superfamily from CATH
  • Summaries and structural analyses of PDB data files from PDBSum
  • Identification of Protein Pockets & Cavities at CASTp
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1lvm_E] [1lvm_C] [1lvm_A] [1lvm] [1lvm_B] [1lvm_D]
  • SWISS-PROT database: [P04517]
  • Domain organization of [POLG_TEV] by SWISSPFAM
  • Other resources with information on 1LVM
  • Community annotation for 1LVM at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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