1V9U Virus Receptor date Feb 03, 2004
title Human Rhinovirus 2 Bound To A Fragment Of Its Cellular Receptor Protein
authors N.Verdaguer, I.Fita, M.Reithmayer, R.Moser, D.Blaas
compound source
Molecule: Coat Protein Vp1
Chain: 1
Synonym: P1d
Organism_scientific: Human Rhinovirus 2
Organism_taxid: 12130
Strain: Serotype 2

Molecule: Coat Protein Vp2
Chain: 2
Synonym: P1b

Organism_scientific: Human Rhinovirus 2
Organism_taxid: 12130
Strain: Serotype 2

Molecule: Coat Protein Vp3
Chain: 3
Synonym: P1c

Organism_scientific: Human Rhinovirus 2
Organism_taxid: 12130
Strain: Serotype 2

Molecule: Coat Protein Vp4
Chain: 4
Synonym: P1a

Organism_scientific: Human Rhinovirus 2
Organism_taxid: 12130
Strain: Serotype 2

Molecule: Ldl-Receptor Class A 3
Chain: 5
Synonym: Vldl-Receptor Module V3
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pmal-C2x
symmetry Space Group: P 21 2 21
R_factor 0.285 R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
313.100 348.790 380.890 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.60 Å
ligand CA, DAO enzyme
Primary referenceX-ray structure of a minor group human rhinovirus bound to a fragment of its cellular receptor protein., Verdaguer N, Fita I, Reithmayer M, Moser R, Blaas D, Nat Struct Mol Biol 2004 May;11(5):429-34. Epub 2004 Apr 4. PMID:15064754
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (142 Kb) [Save to disk]
  • Biological Unit Coordinates (1v9u.pdb1.gz) 7707 Kb
  • LPC: Ligand-Protein Contacts for 1V9U
  • CSU: Contacts of Structural Units for 1V9U
  • Likely Quarternary Molecular Structure file(s) for 1V9U
  • Retrieve 1V9U in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1V9U from S2C, [Save to disk]
  • View 1V9U 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 1V9U
  • VIPERdb: visual, structural and computational analysis of 1V9U
  • Cartoon representation from PDB Cartoon
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1V9U, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1v9u1_, region 1 [Jmol] [rasmolscript] [script source]
        - Domain d1v9u3_, region 3 [Jmol] [rasmolscript] [script source]
        - Domain d1v9u.1, region 4:,2 [Jmol] [rasmolscript] [script source]
        - Domain d1v9u5_, region 5 [Jmol] [rasmolscript] [script source]
  • Fold representative 1v9u from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1v9u_5] [1v9u_3] [1v9u] [1v9u_4] [1v9u_1] [1v9u_2]
  • SWISS-PROT database: [P04936] [P98155]
  • Domain organization of [POLG_HRV2] [VLDLR_HUMAN] by SWISSPFAM
  • Domain found in 1V9U: [LDLa ] by SMART
  • Alignments of the sequence of 1V9U with the sequences similar proteins can be viewed for 1V9U's classification [POLG_HRV2] [VLDLR_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [POLG_HRV2] [VLDLR_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1V9U
  • Community annotation for 1V9U 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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