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 Diffraction	resolution	1.90 Å
ligand	EPE	enzyme
related structures	by homologous chain: 1TJJ
Gene Ontology	Chain Function Process Component A, C, B
Primary reference	Structural 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. On AstexViewer, from MSD-EBI (viewer documentation). On RasMol (Install RasMol freeware) Here's help on how to use RasMol.

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)

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