2RIA Sugar Binding Protein date Oct 10, 2007
title Crystal Structure Of The Trimeric Neck And Carbohydrate Reco Domain Of Human Surfactant Protein D In Complex With D-Glyc Manno-Heptose
authors H.Wang, J.Head, P.Kosma, S.Sheikh, B.Mcdonald, K.Smith, T.Cafarell B.Seaton, E.Crouch
compound source
Molecule: Pulmonary Surfactant-Associated Protein D
Chain: A, B, C
Fragment: Neck And Carbohydrate Recognition 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_plasmid: Pet30a(+)
symmetry Space Group: P 1 21 1
R_factor 0.209 R_Free 0.237
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.414 108.606 55.548 90.00 91.03 90.00
method X-Ray Diffractionresolution 1.80 Å
ligand 289, CA enzyme
Primary referenceRecognition of Heptoses and the Inner Core of Bacterial Lipopolysaccharides by Surfactant Protein D., Wang H, Head J, Kosma P, Brade H, Muller-Loennies S, Sheikh S, McDonald B, Smith K, Cafarella T, Seaton B, Crouch E, Biochemistry. 2008 Jan 15;47(2):710-720. Epub 2007 Dec 20. PMID:18092821
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (81 Kb) [Save to disk]
  • Biological Unit Coordinates (2ria.pdb1.gz) 75 Kb
  • LPC: Ligand-Protein Contacts for 2RIA
  • CSU: Contacts of Structural Units for 2RIA
  • Likely Quarternary Molecular Structure file(s) for 2RIA
  • Structure Factors (871 Kb)
  • Retrieve 2RIA in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2RIA from S2C, [Save to disk]
  • Re-refined 2ria structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2RIA 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 2RIA
  • 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 2RIA, from MSDmotif at EBI
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2ria] [2ria_B] [2ria_A] [2ria_C]
  • SWISS-PROT database: [P35247]
  • Domain organization of [SFTPD_HUMAN] by SWISSPFAM
  • Domain found in 2RIA: [CLECT ] by SMART
  • Other resources with information on 2RIA
  • Community annotation for 2RIA 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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