3TGS Viral Protein date Aug 17, 2011
title Crystal Structure Of Hiv-1 Clade C Strain C1086 Gp120 Core I With Nbd-556
authors Y.D.Kwon, P.D.Kwong
compound source
Molecule: Hiv-1 Clade C1086 Gp120 Core
Chain: A, B
Engineered: Yes
 Organism_scientific: Human Immunodeficiency Virus 1
Organism_common: Hiv-1
Organism_taxid: 11676
Expression_system: Homo Sapiens
Expression_system_taxid: 9606
Expression_system_cell_line: Hek 293
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pvrc8400
symmetry Space Group: C 2 2 21
R_factor 0.239 R_Free 0.295
crystal
cell
length a length b length c angle alpha angle beta angle gamma
66.960 126.000 191.480 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.70 Å
ligand 03G, NAG enzyme
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceUnliganded HIV-1 gp120 core structures assume the CD4-bound conformation with regulation by quaternary interactions and variable loops., Kwon YD, Finzi A, Wu X, Dogo-Isonagie C, Lee LK, Moore LR, Schmidt SD, Stuckey J, Yang Y, Zhou T, Zhu J, Vicic DA, Debnath AK, Shapiro L, Bewley CA, Mascola JR, Sodroski JG, Kwong PD, Proc Natl Acad Sci U S A. 2012 Apr 10;109(15):5663-8. Epub 2012 Mar 26. PMID:22451932
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (244 Kb) [Save to disk]
  • Biological Unit Coordinates (3tgs.pdb1.gz) 236 Kb
  • Biological Unit Coordinates (3tgs.pdb2.gz) 236 Kb
  • LPC: Ligand-Protein Contacts for 3TGS
  • CSU: Contacts of Structural Units for 3TGS
  • Structure Factors (151 Kb)
  • Retrieve 3TGS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3TGS from S2C, [Save to disk]
  • Re-refined 3tgs structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3TGS 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 3TGS
  • 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 3TGS, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3tgs_B] [3tgs_A] [3tgs]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
    • Other resources with information on 3TGS
  • Community annotation for 3TGS at PDBWiki (http://pdbwiki.org)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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