1VFP Hydrolase date Apr 18, 2004
title Crystal Structure Of The Sr Ca2+-Atpase With Bound Amppcp
authors C.Toyoshima, T.Mizutani
compound source
Molecule: Sarcoplasmicendoplasmic Reticulum Calcium Atpase
Chain: A, B
Synonym: Ca2+-Atpase, Serca1
Ec: 3.6.3.8
 Organism_scientific: Oryctolagus Cuniculus
Organism_common: Rabbit
Organism_taxid: 9986
Tissue: Skeletal Muscle (White)
symmetry Space Group: P 1 21 1
R_factor 0.247 R_Free 0.287
crystal
cell
length a length b length c angle alpha angle beta angle gamma
90.920 123.620 151.820 90.00 107.21 90.00
method X-Ray Diffractionresolution 2.90 Å
ligand ACP, CA, MG enzyme Hydrolase E.C.3.6.3.8 BRENDA
related structures by homologous chain: 1T5T, 1WPE
Gene
Ontology
ChainFunctionProcessComponent
A, B


Primary referenceCrystal structure of the calcium pump with a bound ATP analogue., Toyoshima C, Mizutani T, Nature. 2004 Jul 29;430(6999):529-35. Epub 2004 Jun 30. PMID:15229613
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (292 Kb) [Save to disk]
  • Biological Unit Coordinates (1vfp.pdb1.gz) 286 Kb
  • LPC: Ligand-Protein Contacts for 1VFP
  • CSU: Contacts of Structural Units for 1VFP
  • Likely Quarternary Molecular Structure file(s) for 1VFP
  • Retrieve 1VFP in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1VFP from S2C, [Save to disk]
    • View 1VFP 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 1VFP
  • Ramachandran plot from PDBSum
    • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • 3D motif for 1VFP, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1vfpa4, region A:1-124,A:240-343,A:751-994 [Jmol] [rasmolscript] [script source]
        - Domain d1vfpa1, region A:125-239 [Jmol] [rasmolscript] [script source]
        - Domain d1vfpa2, region A:344-360,A:600-750 [Jmol] [rasmolscript] [script source]
        - Domain d1vfpa3, region A:361-599 [Jmol] [rasmolscript] [script source]
        - Domain d1vfpb4, region B:1-124,B:240-343,B:751-994 [Jmol] [rasmolscript] [script source]
        - Domain d1vfpb1, region B:125-239 [Jmol] [rasmolscript] [script source]
        - Domain d1vfpb2, region B:344-360,B:600-750 [Jmol] [rasmolscript] [script source]
        - Domain d1vfpb3, region B:361-599 [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: [1vfp_B] [1vfp] [1vfp_A]
  • SWISS-PROT database: [P04191]
  • Belongs to the p-type atpase (p-atpase) superfamily according to TCDB.
  • Domain organization of [AT2A1_RABIT] by SWISSPFAM
  • Domain found in 1VFP: [Cation_ATPase_N ] by SMART
    • Other resources with information on 1VFP
  • Community annotation for 1VFP 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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