1U8H Immune System date Aug 06, 2004
title Crystal Structure Of The Hiv-1 Cross Neutralizing Monoclonal Antibody 2f5 In Complex With Gp41 Peptide Aldkwas
authors S.Bryson, J.P.Julien, R.C.Hynes, E.F.Pai
compound source
Molecule: Antibody 2f5 (Light Chain)
Chain: A
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Antibody 2f5 (Heavy Chain)
Chain: B
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606

Molecule: Gp41 Peptide
Chain: C
Engineered: Yes
Synthetic: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Other_details: Synthetic Peptide
symmetry Space Group: P 21 21 21
R_factor 0.221 R_Free 0.236
crystal
cell
length a length b length c angle alpha angle beta angle gamma
58.100 64.900 175.600 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.10 Å
related structures by homologous chain: 1FL5, 1I8M, 1TJH
Primary referenceCrystallographic definition of the epitope promiscuity of the broadly neutralizing anti-human immunodeficiency virus type 1 antibody 2F5: vaccine design implications., Bryson S, Julien JP, Hynes RC, Pai EF, J Virol. 2009 Nov;83(22):11862-75. Epub 2009 Sep 9. PMID:19740978
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (80 Kb) [Save to disk]
  • Biological Unit Coordinates (1u8h.pdb1.gz) 75 Kb
  • CSU: Contacts of Structural Units for 1U8H
  • Likely Quarternary Molecular Structure file(s) for 1U8H
  • Structure Factors (616 Kb)
  • Retrieve 1U8H in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1U8H from S2C, [Save to disk]
  • Re-refined 1u8h structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1U8H 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 1U8H
  • 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 1U8H, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1u8ha1, region A:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1u8ha2, region A:107-214 [Jmol] [rasmolscript] [script source]
        - Domain d1u8hb1, region B:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1u8hb2, region B:114-216 [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: [1u8h] [1u8h_A] [1u8h_C] [1u8h_B]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 1U8H: [IG_like] [IGv ] by SMART
    • Other resources with information on 1U8H
  • Community annotation for 1U8H 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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