1RZI Crystal structure of human anti-HIV-1 gp120-reactive antibody 47e fab date
authors Huang, C.C., Venturi, M., Majeed, S., Moore, M.J., Phogat, S., Zhang, M.Y., Dimitrov, D.S., Hendrickson, W.A., Robinson, J., Sodroski, J., Wyatt, R., Choe, H., Farzan, M., Kwong, P.D.
compound source
R_Free 0.321
length a length b length c angle alpha angle beta angle gamma
method X-Ray Diffractionresolution 2.90
related structures by homologous chain: 1AIF, 1FSK, 1G9N, 1KYO
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] (538 Kb) [Save to disk]
  • Biological Unit Coordinates (1rzi.pdb1.gz) 74 Kb
  • Biological Unit Coordinates (1rzi.pdb2.gz) 75 Kb
  • Biological Unit Coordinates (1rzi.pdb3.gz) 74 Kb
  • Biological Unit Coordinates (1rzi.pdb4.gz) 74 Kb
  • Biological Unit Coordinates (1rzi.pdb5.gz) 74 Kb
  • Biological Unit Coordinates (1rzi.pdb6.gz) 73 Kb
  • Biological Unit Coordinates (1rzi.pdb7.gz) 74 Kb
  • Biological Unit Coordinates (1rzi.pdb8.gz) 74 Kb
  • CSU: Contacts of Structural Units for 1RZI
  • Likely Quarternary Molecular Structure file(s) for 1RZI
  • Structure Factors (1209 Kb)
  • Retrieve 1RZI in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1RZI from S2C, [Save to disk]
  • Re-refined 1rzi structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1RZI 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 1RZI
  • 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 1RZI, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1rzia2, region A:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzia1, region A:2-107 [Jmol] [rasmolscript] [script source]
        - Domain d1rzib1, region B:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1rzib2, region B:114-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzic1, region C:1-107 [Jmol] [rasmolscript] [script source]
        - Domain d1rzic2, region C:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzid1, region D:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1rzid2, region D:114-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzie2, region E:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzie1, region E:2-107 [Jmol] [rasmolscript] [script source]
        - Domain d1rzif1, region F:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1rzif2, region F:114-214 [Jmol] [rasmolscript] [script source]
        - Domain d1rzig2, region G:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzig1, region G:2-107 [Jmol] [rasmolscript] [script source]
        - Domain d1rzih1, region H:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1rzih2, region H:114-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzii2, region I:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzii1, region I:2-107 [Jmol] [rasmolscript] [script source]
        - Domain d1rzij1, region J:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1rzij2, region J:114-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzik2, region K:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzik1, region K:2-107 [Jmol] [rasmolscript] [script source]
        - Domain d1rzil1, region L:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1rzil2, region L:114-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzim2, region M:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzim1, region M:2-107 [Jmol] [rasmolscript] [script source]
        - Domain d1rzin1, region N:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1rzin2, region N:114-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzio2, region O:108-213 [Jmol] [rasmolscript] [script source]
        - Domain d1rzio1, region O:2-107 [Jmol] [rasmolscript] [script source]
        - Domain d1rzip1, region P:1-113 [Jmol] [rasmolscript] [script source]
        - Domain d1rzip2, region P:114-213 [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: [1rzi_J] [1rzi_I] [1rzi_D] [1rzi_F] [1rzi_H] [1rzi_E] [1rzi_O] [1rzi_K] [1rzi_B] [1rzi_A] [1rzi_G] [1rzi_C] [1rzi] [1rzi_M] [1rzi_L] [1rzi_P] [1rzi_N]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domains found in 1RZI: [IG_like] [IGv ] by SMART
  • Other resources with information on 1RZI
  • Community annotation for 1RZI 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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