1PUB Lipid Binding Protein date Jun 24, 2003
title Gm2-Activator Protein Crystal Structure
authors C.S.Wright, Q.Zhao, F.Rastinejad
compound source
Molecule: Gm2-Activator Protein
Chain: A
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: Pt513
symmetry Space Group: P 21 21 21
R_factor 0.209 R_Free 0.286
crystal
cell
length a length b length c angle alpha angle beta angle gamma
40.070 42.420 113.780 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.51 Å
ligand 3PH enzyme
related structures by homologous chain: 1G13
subcellular loc. Membrane localization by OPM: Lysosome membrane
Gene
Ontology
ChainFunctionProcessComponent
A


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] (33 Kb) [Save to disk]
  • Biological Unit Coordinates (1pub.pdb1.gz) 28 Kb
  • LPC: Ligand-Protein Contacts for 1PUB
  • CSU: Contacts of Structural Units for 1PUB
  • Likely Quarternary Molecular Structure file(s) for 1PUB
  • Structure Factors (78 Kb)
  • Retrieve 1PUB in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1PUB from S2C, [Save to disk]
  • Re-refined 1pub structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1PUB 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 1PUB
  • 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 1PUB, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1puba_, region A [Jmol] [rasmolscript] [script source]
  • Fold representative 1pub 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: [1pub_A] [1pub]
  • SWISS-PROT database: [P17900]
  • Domain organization of [SAP3_HUMAN] by SWISSPFAM
  • Domain found in 1PUB: [ML ] by SMART
  • Alignments of the sequence of 1PUB with the sequences similar proteins can be viewed for 1PUB'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 1PUB
  • Community annotation for 1PUB 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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