1N69 Lipid Binding Protein date Nov 08, 2002
title Crystal Structure Of Human Saposin B
authors V.E.Ahn, K.F.Faull, J.P.Whitelegge, A.L.Fluharty, G.G.Prive
compound source
Molecule: Saposin B
Chain: A, B, C
Synonym: Proactivator Polypeptide, Sap-B, Sphingolipid Activator Protein 1, Sap-1, Cerebroside Sulfate Activator, Csact, Cs-Act, Sulfatidegm1 Activator, Galactosylcerbroside Activator;
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Prosaposin, Psap
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Ad494(De3)
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet-16(B)
symmetry Space Group: P 31 2 1
R_factor 0.222 R_Free 0.262
crystal
cell
length a length b length c angle alpha angle beta angle gamma
72.140 72.140 94.366 90.00 90.00 120.00
method X-Ray Diffractionresolution 2.20 Å
ligand PEH enzyme
subcellular loc. Membrane localization by OPM: Lysosome membrane
Primary referenceCrystal structure of saposin B reveals a dimeric shell for lipid binding., Ahn VE, Faull KF, Whitelegge JP, Fluharty AL, Prive GG, Proc Natl Acad Sci U S A 2003 Jan 7;100(1):38-43. PMID:12518053
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (45 Kb) [Save to disk]
  • Biological Unit Coordinates (1n69.pdb1.gz) 28 Kb
  • Biological Unit Coordinates (1n69.pdb2.gz) 27 Kb
  • LPC: Ligand-Protein Contacts for 1N69
  • CSU: Contacts of Structural Units for 1N69
  • Likely Quarternary Molecular Structure file(s) for 1N69
  • Structure Factors (122 Kb)
  • Retrieve 1N69 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1N69 from S2C, [Save to disk]
  • Re-refined 1n69 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1N69 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 1N69
  • 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 1N69, from MSDmotif at EBI
  • Classification of representative domains in scop (Structural Classification of Proteins)
        - Domain d1n69a_, region A [Jmol] [rasmolscript] [script source]
        - Domain d1n69b_, region B [Jmol] [rasmolscript] [script source]
        - Domain d1n69c_, region C [Jmol] [rasmolscript] [script source]
  • Fold representative 1n69 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: [1n69_C] [1n69_A] [1n69] [1n69_B]
  • SWISS-PROT database: [P07602]
  • Belongs to the amoebapore (amoebapore) family according to TCDB.
  • Domain organization of [SAP_HUMAN] by SWISSPFAM
  • Domain found in 1N69: [SapB ] by SMART
  • Alignments of the sequence of 1N69 with the sequences similar proteins can be viewed for 1N69's classification [SAP_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 [SAP_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1N69
  • Community annotation for 1N69 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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