2AF9 Lipid Binding Protein date Jul 25, 2005
title Crystal Structure Analysis Of Gm2-Activator Protein Complexed With Phosphatidylcholine
authors C.S.Wright, L.Z.Mi, S.Lee, F.Rastinejad
compound source
Molecule: Ganglioside Gm2 Activator
Chain: A
Synonym: Gm2-Ap
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Liver, Brain, Neurons
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 0.222 R_Free 0.279
crystal
cell
length a length b length c angle alpha angle beta angle gamma
39.120 41.980 114.210 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand DAO, IPA, MYR, OLA enzyme
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceCrystal Structure Analysis of Phosphatidylcholine-GM2-Activator Product Complexes: Evidence for Hydrolase Activity(,)., Wright CS, Mi LZ, Lee S, Rastinejad F, Biochemistry 2005 Oct 18;44(41):13510-21. PMID:16216074
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (35 Kb) [Save to disk]
  • Biological Unit Coordinates (2af9.pdb1.gz) 30 Kb
  • LPC: Ligand-Protein Contacts for 2AF9
  • CSU: Contacts of Structural Units for 2AF9
  • Likely Quarternary Molecular Structure file(s) for 2AF9
  • Structure Factors (143 Kb)
  • Retrieve 2AF9 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2AF9 from S2C, [Save to disk]
  • Re-refined 2af9 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2AF9 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 2AF9
  • 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 2AF9, from MSDmotif at EBI
  • Fold representative 2af9 from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2af9] [2af9_A]
  • SWISS-PROT database: [P17900]
  • Domain organization of [SAP3_HUMAN] by SWISSPFAM
  • Domain found in 2AF9: [ML ] by SMART
  • Alignments of the sequence of 2AF9 with the sequences similar proteins can be viewed for 2AF9'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 2AF9
  • Community annotation for 2AF9 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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