2YAD Surfactant Protein date Feb 18, 2011
title Brichos Domain Of Surfactant Protein C Precursor Protein
authors G.Askarieh, M.I.Siponen, H.Willander, M.Landreh, P.Westermark, K. H.Keranen, E.Hermansson, A.Hamvas, L.M.Nogee, T.Bergman, A.Saenz C.Casals, J.Aqvist, H.Jornvall, J.Presto, J.Johansson, C.H.Arrow C.Bountra, R.Collins, A.M.Edwards, T.Ekblad, S.Flodin, A.Flores, S.Graslund, M.Hammarstrom, I.Johansson, T.Karlberg, S.Kol, T.Kot E.Kouznetsova, M.Moche, T.Nyman, P.Nordlund, C.Persson, H.Schule A.G.Thorsell, L.Tresaugues, S.Van Den Berg, E.Wahlberg, J.Weige M.Welin, H.Berglund, S.D.Knight
compound source
Molecule: Surfactant Protein C Brichos Domain
Chain: A, B, C, D, E, F
Fragment: Residues 15-144
Engineered: Yes
Other_details: Expressed N-Terminal Sequence Differs From U Reference
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Expression_system: Escherichia Coli
Expression_system_taxid: 83333
Expression_system_strain: Origami B(De3)
Expression_system_variant: Plyss
symmetry Space Group: C 1 2 1
R_factor 0.1902 R_Free 0.2221
crystal
cell
length a length b length c angle alpha angle beta angle gamma
132.046 39.329 114.756 90.00 99.63 90.00
method X-Ray Diffractionresolution 2.20 Å
ligand MSE enzyme
note 2YAD is a representative structure
Primary referenceHigh-resolution structure of a BRICHOS domain and its implications for anti-amyloid chaperone activity on lung surfactant protein C., Willander H, Askarieh G, Landreh M, Westermark P, Nordling K, Keranen H, Hermansson E, Hamvas A, Nogee LM, Bergman T, Saenz A, Casals C, Aqvist J, Jornvall H, Berglund H, Presto J, Knight SD, Johansson J, Proc Natl Acad Sci U S A. 2012 Feb 2. PMID:22308375
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (165 Kb) [Save to disk]
  • Biological Unit Coordinates (2yad.pdb1.gz) 77 Kb
  • Biological Unit Coordinates (2yad.pdb2.gz) 80 Kb
  • LPC: Ligand-Protein Contacts for 2YAD
  • CSU: Contacts of Structural Units for 2YAD
  • Structure Factors (1416 Kb)
  • Retrieve 2YAD in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 2YAD from S2C, [Save to disk]
  • Re-refined 2yad structure from PDB_REDO, a databank with updated and optimised macromolecular X-ray diffraction structure models
  • View 2YAD 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 2YAD
  • 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 2YAD, from MSDmotif at EBI
  • Fold representative 2yad from FSSP and Dali (Families of Structurally Similar Proteins)
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [2yad_B] [2yad_D] [2yad_F] [2yad_E] [2yad_A] [2yad] [2yad_C]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Domain found in 2YAD: [BRICHOS ] by SMART
  • Other resources with information on 2YAD
  • Community annotation for 2YAD at PDBWiki (http://pdbwiki.org)
  • Movements, Movies and Images
  • Images from IMB Jena Image Library of Biological Macromolecules.

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