3G83 Sugar Binding Protein date Feb 11, 2009
title Crystal Structure Of The Trimeric Neck And Carbohydrate Reco Domain Of Human Surfactant Protein D In Complex With Alpha Dimannose.
authors J.F.Head
compound source
Molecule: Pulmonary Surfactant-Associated Protein D
Chain: A, B, C
Fragment: Unp Residues 223-375
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: Rosetta Blue
Expression_system_vector_type: Plasmid
Expression_system_plasmid: Pet30a (+)
symmetry Space Group: P 1 21 1
R_factor 0.189 R_Free 0.215
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.754 108.774 56.011 90.00 91.58 90.00
method X-Ray Diffractionresolution 1.90 Å
ligand CA, MAN enzyme
Primary referenceRecognition of Mannosylated Ligands and Influenza A Virus by Human SP-D: Contributions of an Extended Site and Residue 343., Crouch E, Hartshorn K, Horlacher T, McDonald B, Smith K, Cafarella T, Seaton B, Seeberger P, Head J, Biochemistry. 2009 Feb 27. PMID:19249874
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (86 Kb) [Save to disk]
  • Biological Unit Coordinates (3g83.pdb1.gz) 81 Kb
  • LPC: Ligand-Protein Contacts for 3G83
  • CSU: Contacts of Structural Units for 3G83
  • Likely Quarternary Molecular Structure file(s) for 3G83
  • Structure Factors (470 Kb)
  • Retrieve 3G83 in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 3G83 from S2C, [Save to disk]
  • Re-refined 3g83 structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
    • View 3G83 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 3G83
  • 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 3G83, from MSDmotif at EBI
    • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [3g83_A] [3g83_C] [3g83_B] [3g83]
  • SWISS-PROT database: [P35247]
  • Domain organization of [SFTPD_HUMAN] by SWISSPFAM
  • Domain found in 3G83: [CLECT ] by SMART
    • Other resources with information on 3G83
  • Community annotation for 3G83 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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