1M9Y Isomerase Viral Protein date Jul 30, 2002
title X-Ray Crystal Structure Of Cyclophilin Ahiv-1 Ca N-Terminal (1-146) M-Type H87a,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
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 0.162 R_Free 0.234
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.426 111.223 67.780 89.99 101.45 89.75
method X-Ray Diffractionresolution 1.90 Å
ligand
enzyme Isomerase E.C.5.2.1.8 BRENDA
related structures by homologous chain: 1CWI, 1M9D, 1M9F
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] (213 Kb) [Save to disk]
  • Biological Unit Coordinates (1m9y.pdb1.gz) 52 Kb
  • Biological Unit Coordinates (1m9y.pdb2.gz) 56 Kb
  • Biological Unit Coordinates (1m9y.pdb3.gz) 54 Kb
  • Biological Unit Coordinates (1m9y.pdb4.gz) 54 Kb
  • CSU: Contacts of Structural Units for 1M9Y
  • Likely Quarternary Molecular Structure file(s) for 1M9Y
  • Structure Factors (625 Kb)
  • Retrieve 1M9Y in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1M9Y from S2C, [Save to disk]
  • Re-refined 1m9y structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 1M9Y 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 1M9Y
  • 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 1M9Y, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1m9ya_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1m9yb_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1m9yc_, region C [Jmol] [rasmolscript] [script source]
        - Domain d1m9yd_, region D [Jmol] [rasmolscript] [script source]
        - Domain d1m9ye_, region E [Jmol] [rasmolscript] [script source]
        - Domain d1m9yf_, region F [Jmol] [rasmolscript] [script source]
        - Domain d1m9yg_, region G [Jmol] [rasmolscript] [script source]
        - Domain d1m9yh_, 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: [1m9y_E] [1m9y_H] [1m9y_B] [1m9y_G] [1m9y_A] [1m9y_F] [1m9y_C] [1m9y] [1m9y_D]
  • SWISS-PROT database: [P62937] [Q72497]
  • Domain organization of [PPIA_HUMAN] [Q72497_9HIV1] by SWISSPFAM
    • Other resources with information on 1M9Y
  • Community annotation for 1M9Y 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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