1G13 Ligand Binding Protein date Oct 10, 2000
title Human Gm2 Activator Structure
authors C.S.Wright, S.C.Li, F.Rastinejad
compound source
Molecule: Ganglioside M2 Activator Protein
Chain: A, B, C
Fragment: Residues 39-200
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Organ: Kidney
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_vector_type: Pt7-7
Expression_system_vector: Plasmid
symmetry Space Group: P 21 21 21
R_factor 0.215 R_Free 0.258
crystal
cell
length a length b length c angle alpha angle beta angle gamma
63.420 85.630 120.070 90.00 90.00 90.00
method X-Ray Diffractionresolution 2.00 Å
ligand EPE, MSE enzyme
related structures by homologous chain: 1PUB, 1TJJ
Gene
Ontology
ChainFunctionProcessComponent
A, C, B


Primary referenceCrystal structure of human GM2-activator protein with a novel beta-cup topology., Wright CS, Li SC, Rastinejad F, J Mol Biol 2000 Dec 1;304(3):411-22. PMID:11090283
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (88 Kb) [Save to disk]
  • Biological Unit Coordinates (1g13.pdb1.gz) 30 Kb
  • Biological Unit Coordinates (1g13.pdb2.gz) 30 Kb
  • Biological Unit Coordinates (1g13.pdb3.gz) 29 Kb
  • Biological Unit Coordinates (1g13.pdb4.gz) 57 Kb
  • LPC: Ligand-Protein Contacts for 1G13
  • CSU: Contacts of Structural Units for 1G13
  • Likely Quarternary Molecular Structure file(s) for 1G13
  • Structure Factors (357 Kb)
  • Retrieve 1G13 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1G13 from S2C, [Save to disk]
  • Re-refined 1g13 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1G13 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 1G13
  • 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 1G13, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1g13a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1g13b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1g13c_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1g13 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: [1g13_A] [1g13_B] [1g13_C] [1g13]
  • SWISS-PROT database: [P17900]
  • Domain organization of [SAP3_HUMAN] by SWISSPFAM
  • Domain found in 1G13: [ML ] by SMART
  • Alignments of the sequence of 1G13 with the sequences similar proteins can be viewed for 1G13'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 1G13
  • Community annotation for 1G13 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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