1M9X Isomerase Viral Protein date Jul 30, 2002
title X-Ray Crystal Structure Of Cyclophilin Ahiv-1 Ca N-Terminal (1-146) M-Type H87a,A88m,G89a Complex.
authors B.R.Howard, F.F.Vajdos, S.Li, W.I.Sundquist, C.P.Hill
compound source
Molecule: Cyclophilin A
Chain: A, B, E, F
Synonym: Peptidyl-Prolyl Cis-Trans Isomerase A, Ppiase, Rot Cyclosporin A-Binding Protein;
Ec: 5.2.1.8
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet3a

Molecule: Hiv-1 Capsid
Chain: C, D, G, H
Fragment: N-Terminal Domain
Engineered: Yes
Mutation: Yes
Organism_scientific: Human Immunodeficiency Virus 1
Organism_taxid: 11676
Gene: Ca
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet11a
symmetry Space Group: P 1
R_factor 0.165 R_Free 0.230
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.467 111.118 67.910 89.98 101.60 89.90
method X-Ray Diffractionresolution 1.70 Å
ligand
enzyme Isomerase E.C.5.2.1.8 BRENDA
related structures by homologous chain: 1M9E, 1W8M, 1W8V
Gene
Ontology
ChainFunctionProcessComponent
F, A, E, B


H, C, D, G


Primary referenceStructural insights into the catalytic mechanism of cyclophilin A., Howard BR, Vajdos FF, Li S, Sundquist WI, Hill CP, Nat Struct Biol 2003 Jun;10(6):475-81. PMID:12730686
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (222 Kb) [Save to disk]
  • Biological Unit Coordinates (1m9x.pdb1.gz) 55 Kb
  • Biological Unit Coordinates (1m9x.pdb2.gz) 58 Kb
  • Biological Unit Coordinates (1m9x.pdb3.gz) 56 Kb
  • Biological Unit Coordinates (1m9x.pdb4.gz) 56 Kb
  • CSU: Contacts of Structural Units for 1M9X
  • Likely Quarternary Molecular Structure file(s) for 1M9X
  • Structure Factors (862 Kb)
  • Retrieve 1M9X in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M9X from S2C, [Save to disk]
  • Re-refined 1m9x structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1M9X 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 1M9X
  • 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 1M9X, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m9xa_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1m9xb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1m9xc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1m9xd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1m9xe_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1m9xf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1m9xg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1m9xh_, region H [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: [1m9x_H] [1m9x_F] [1m9x_B] [1m9x_G] [1m9x] [1m9x_E] [1m9x_D] [1m9x_C] [1m9x_A]
  • SWISS-PROT database: [P62937] [Q72497]
  • Domain organization of [PPIA_HUMAN] [Q72497_9HIV1] by SWISSPFAM
    • Other resources with information on 1M9X
  • Community annotation for 1M9X at PDBWiki (http://pdbwiki.org)
  • MMDB (Entrez's Structure Database)
    • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

    • You may enter another PDB ID code
    Go [Back], to the [PDB Lite page], to the [OCA Search page] or to the [PDB Home page]
    OCA© by Jaime Prilusky, 1996-2014,2022
    Bioinformatics Unit
    Weizmann Institute of Science