2ORK Sugar Binding Protein date Feb 02, 2007
title Crystal Structure Of The Trimeric Neck And Carbohydrate Reco Domain Of Human Surfactant Protein D In Complex With Inosit Phosphate
authors J.F.Head
compound source
Molecule: Pulmonary Surfactant-Associated Protein D
Chain: A, B, C
Fragment: Head And Neck Domain
Synonym: Sp-D, Psp-D, Lung Surfactant Protein D
Engineered: Yes
 Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sftpd, Pspd, Sftp4
Expression_system: Escherichia Coli
Expression_system_taxid: 562
Expression_system_strain: Rosettablue
Expression_system_vector_type: Plasmid
Expression_system_vector: Pet30a(+)
symmetry Space Group: P 1 21 1
R_factor 0.186 R_Free 0.226
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.403 108.010 55.701 90.00 91.83 90.00
method X-Ray Diffractionresolution 1.89 Å
ligand CA, IPD enzyme
Primary referenceCritical Role of Arg/Lys343 in the Species-Dependent Recognition of Phosphatidylinositol by Pulmonary Surfactant Protein D(,)., Crouch E, McDonald B, Smith K, Roberts M, Mealy T, Seaton B, Head J, Biochemistry. 2007 May 1;46(17):5160-5169. Epub 2007 Apr 7. PMID:17417879
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (2ork.pdb1.gz) 80 Kb
  • LPC: Ligand-Protein Contacts for 2ORK
  • CSU: Contacts of Structural Units for 2ORK
  • Likely Quarternary Molecular Structure file(s) for 2ORK
  • Structure Factors (765 Kb)
  • Retrieve 2ORK in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2ORK from S2C, [Save to disk]
  • Re-refined 2ork structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 2ORK 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 2ORK
  • 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
  • 3D motif for 2ORK, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ork] [2ork_B] [2ork_A] [2ork_C]
  • SWISS-PROT database: [P35247]
  • Domain organization of [SFTPD_HUMAN] by SWISSPFAM
  • Domain found in 2ORK: [CLECT ] by SMART
    • Other resources with information on 2ORK
  • Community annotation for 2ORK 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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