1RZ7 Immune System date Dec 24, 2003
title Crystal Structure Of Human Anti-Hiv-1 Gp120-Reactive Antibod
authors C.C.Huang, M.Venturi, S.Majeed, M.J.Moore, S.Phogat, M.Y.Zhang, D.S.Dimitrov, W.A.Hendrickson, J.Robinson, J.Sodroski, R.Wyatt, M.Farzan, P.D.Kwong
compound source
Molecule: Fab 48d Light Chain
Chain: L
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Human Herpesvirus 4
Expression_system_common: Epstein-Barr Virus
Expression_system_taxid: 10376
Expression_system_cell: Immortalized B-Cell Clone Fused Wit Murine B-Cell Fusion Partner;

Molecule: Fab 48d Heavy Chain
Chain: H
Engineered: Yes

Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Human Herpesvirus 4
Expression_system_common: Epstein-Barr Virus
Expression_system_taxid: 10376
Expression_system_cell: Immortalized B-Cell Clone Fused Wit Murine B-Cell Fusion Partner
symmetry Space Group: P 21 21 21
R_factor 0.201 R_Free 0.231
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.485 72.951 101.921 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand GOL enzyme
related structures by homologous chain: 1IQD, 1RZG, 1TJG
Primary referenceStructural basis of tyrosine sulfation and VH-gene usage in antibodies that recognize the HIV type 1 coreceptor-binding site on gp120., Huang CC, Venturi M, Majeed S, Moore MJ, Phogat S, Zhang MY, Dimitrov DS, Hendrickson WA, Robinson J, Sodroski J, Wyatt R, Choe H, Farzan M, Kwong PD, Proc Natl Acad Sci U S A 2004 Mar 2;101(9):2706-11. Epub 2004 Feb 23. PMID:14981267
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (75 Kb) [Save to disk]
  • Biological Unit Coordinates (1rz7.pdb1.gz) 70 Kb
  • LPC: Ligand-Protein Contacts for 1RZ7
  • CSU: Contacts of Structural Units for 1RZ7
  • Likely Quarternary Molecular Structure file(s) for 1RZ7
  • Structure Factors (264 Kb)
  • Retrieve 1RZ7 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RZ7 from S2C, [Save to disk]
  • Re-refined 1rz7 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RZ7 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 1RZ7
  • 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 1RZ7, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rz7h1, region H:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1rz7h2, region H:114-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rz7l2, region L:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rz7l1, region L:2-107 [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: [1rz7_H] [1rz7] [1rz7_L]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 1RZ7: [IG_like] [IGv ] by SMART
  • Other resources with information on 1RZ7
  • Community annotation for 1RZ7 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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