1PU5 Lipid Binding Protein date Jun 24, 2003
title Gm2-Activator Protein Crystal Structure
authors C.S.Wright, Q.Zhao, F.Rastinejad
compound source
Molecule: Ganglioside Gm2 Activator
Chain: A, B, C
Synonym: Gm2-Ap, Cerebroside Sulfate Activator Protein, Shingolipid Activator Protein 3, Sap-3;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Gm2a
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_strain: Bl21(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet16b (Novagen)
symmetry Space Group: P 21 21 21
R_factor 0.214 R_Free 0.253
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.320 86.130 120.210 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand EPE enzyme
related structures by homologous chain: 1TJJ
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceStructural analysis of lipid complexes of GM2-activator protein., Wright CS, Zhao Q, Rastinejad F, J Mol Biol 2003 Aug 22;331(4):951-64. PMID:12909021
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (1pu5.pdb1.gz) 30 Kb
  • Biological Unit Coordinates (1pu5.pdb2.gz) 30 Kb
  • Biological Unit Coordinates (1pu5.pdb3.gz) 29 Kb
  • Biological Unit Coordinates (1pu5.pdb4.gz) 58 Kb
  • LPC: Ligand-Protein Contacts for 1PU5
  • CSU: Contacts of Structural Units for 1PU5
  • Likely Quarternary Molecular Structure file(s) for 1PU5
  • Structure Factors (583 Kb)
  • Retrieve 1PU5 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PU5 from S2C, [Save to disk]
  • Re-refined 1pu5 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PU5 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 1PU5
  • Cartoon representation from PDB Cartoon
  • 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
  • Crystal Contacts, from CryCo at Weizmann Institute
  • 3D motif for 1PU5, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1pu5a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1pu5b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1pu5c_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1pu5 from FSSP and Dali (Families of Structurally Similar Proteins)
  • 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: [1pu5_A] [1pu5] [1pu5_C] [1pu5_B]
  • SWISS-PROT database: [P17900]
  • Domain organization of [SAP3_HUMAN] by SWISSPFAM
  • Domain found in 1PU5: [ML ] by SMART
  • Alignments of the sequence of 1PU5 with the sequences similar proteins can be viewed for 1PU5's classification [SAP3_HUMAN] at ProtoMap. Click on "Neighbors List", then on the "See Alignments" button below the list.
  • A sequence distance tree ("phylogenetic tree") can be viewed for 1ACL's classification [SAP3_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1PU5
  • Community annotation for 1PU5 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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