1XPH Immune System, Sugar Binding Protein date Oct 08, 2004
title Structure Of Dc-Signr And A Portion Of Repeat Domain 8
authors G.A.Snyder, M.Colonna, P.D.Sun
compound source
Molecule: Cd209 Antigen-Like Protein 1
Chain: A
Fragment: Sequence Database Residues 250-399: Contains C- Type Lectin Domain (Residues 274-390);
Synonym: Dendritic Cell-Specific Icam-3 Non-Integrin Related Dc-Signr, Carbohydrate Recognition Domain And Repeat 8 Of Dc-Signr, Dendritic Cell-Specific Icam-3- Grabbing Nonintegrin 2, Dc-Sign2, Dc-Sign Related Protein, Dc-Signr, Liverlymph Node Specific Icam-3-Grabbing Nonintegrin, L-Sign;
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: Pet22b
symmetry Space Group: P 21 21 21
R_factor 0.176 R_Free 0.193
crystal
cell
length a length b length c angle alpha angle beta angle gamma
38.233 54.887 62.352 90.00 90.00 90.00
method X-Ray Diffractionresolution 1.41 Å
ligand CA enzyme
related structures by homologous chain: 1SL4
Gene
Ontology
ChainFunctionProcessComponent
A


Primary referenceThe structure of DC-SIGNR with a portion of its repeat domain lends insights to modeling of the receptor tetramer., Snyder GA, Colonna M, Sun PD, J Mol Biol. 2005 Apr 15;347(5):979-89. PMID:15784257
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (30 Kb) [Save to disk]
  • Biological Unit Coordinates (1xph.pdb1.gz) 26 Kb
  • LPC: Ligand-Protein Contacts for 1XPH
  • CSU: Contacts of Structural Units for 1XPH
  • Likely Quarternary Molecular Structure file(s) for 1XPH
  • Structure Factors (176 Kb)
  • Retrieve 1XPH in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 1XPH from S2C, [Save to disk]
  • Re-refined 1xph structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 1XPH 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 1XPH
  • 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 1XPH, from MSDmotif at EBI
  • Fold representative 1xph from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [1xph_A] [1xph]
  • SWISS-PROT database: [Q9H2X3]
  • Domain organization of [CLC4M_HUMAN] by SWISSPFAM
  • Domain found in 1XPH: [CLECT ] by SMART
  • Alignments of the sequence of 1XPH with the sequences similar proteins can be viewed for 1XPH's classification [CLC4M_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 [CLC4M_HUMAN] at ProtoMap. Click on the Cluster number.
  • Other resources with information on 1XPH
  • Community annotation for 1XPH 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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