3DPR Virus date Jul 09, 2008
title Human Rhinovirus 2 Bound To A Concatamer Of The Vldl Recepto V3
authors J.Querol-Audi, J.Pous, I.Fita, N.Verdaguer
compound source
Molecule: Protein Vp1
Chain: A
Synonym: Virion Protein 1, P1d, Coat Protein Vp1
Organism_scientific: Human Rhinovirus 2
Organism_common: Hrv-2
Organism_taxid: 12130
Strain: Human
Other_details: Hela Cells

Molecule: Protein Vp2
Chain: B
Synonym: Virion Protein 2, P1b, Coat Protein Vp2

Organism_scientific: Human Rhinovirus 2
Organism_common: Hrv-2
Organism_taxid: 12130
Strain: Human
Other_details: Hela Cells

Molecule: Protein Vp3
Chain: C
Synonym: Virion Protein 3, P1c, Coat Protein Vp3

Organism_scientific: Human Rhinovirus 2
Organism_common: Hrv-2
Organism_taxid: 12130
Strain: Human
Other_details: Hela Cells

Molecule: Protein Vp4
Chain: D
Synonym: Virion Protein 4, P1a, Coat Protein Vp4

Organism_scientific: Human Rhinovirus 2
Organism_common: Hrv-2
Organism_taxid: 12130
Strain: Human
Other_details: Hela Cells

Molecule: Ldl-Receptor Class A 3
Chain: E
Synonym: Vldl-Receptor Module 3, V33333
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 43 21 2
R_factor 0.425 R_Free 0.441
crystal
cell
length a length b length c angle alpha angle beta angle gamma
498.117 498.117 658.425 90.00 90.00 90.00
method X-Ray Diffractionresolution 3.50 Å
ligand CA, DAO enzyme
Primary referenceMinor group human rhinovirus-receptor interactions: geometry of multimodular attachment and basis of recognition., Querol-Audi J, Konecsni T, Pous J, Carugo O, Fita I, Verdaguer N, Blaas D, FEBS Lett. 2009 Jan 5;583(1):235-40. Epub 2008 Dec 13. PMID:19073182
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (111 Kb) [Save to disk]
  • Biological Unit Coordinates (3dpr.pdb1.gz) 6557 Kb
  • LPC: Ligand-Protein Contacts for 3DPR
  • CSU: Contacts of Structural Units for 3DPR
  • Likely Quarternary Molecular Structure file(s) for 3DPR
  • Structure Factors (11302 Kb)
  • Retrieve 3DPR in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3DPR from S2C, [Save to disk]
  • Re-refined 3dpr structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 3DPR 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 3DPR
  • VIPERdb: visual, structural and computational analysis of 3DPR
  • 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 3DPR, from MSDmotif at EBI
  • Fold representative 3dpr from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3dpr] [3dpr_A] [3dpr_E] [3dpr_D] [3dpr_B] [3dpr_C]
  • SWISS-PROT database: [P04936] [P98155]
  • Domain organization of [POLG_HRV2] [VLDLR_HUMAN] by SWISSPFAM
  • Domain found in 3DPR: [LDLa ] by SMART
  • Other resources with information on 3DPR
  • Community annotation for 3DPR 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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