5OXS Surfactant Protein date Sep 07, 2017
title Crystal Structure Of Human Lung Surfactant Protein D Trimeri With Bound Ligand Salmonella Enterica Minnesota R5 Oligosac
authors A.K.Shrive, T.J.Greenhough
compound source
Molecule: Pulmonary Surfactant-Associated Protein D
Chain: A, B, C
Fragment: Trimeric Neck + Carbohydrate Recognition Domain
Synonym: Sp-D,Collectin-7,Lung Surfactant Protein D
Engineered: Yes
Organism_scientific: Homo Sapiens
Organism_common: Human
Organism_taxid: 9606
Gene: Sftpd, Colec7, Pspd, Sftp4
Expression_system: Escherichia Coli Bl21(De3)
Expression_system_taxid: 469008
Expression_system_vector_type: Plasmid
symmetry Space Group: P 1 21 1
R_factor 0.165 R_Free 0.187
crystal
cell
length a length b length c angle alpha angle beta angle gamma
55.679 108.510 56.170 90.00 92.89 90.00
method X-Ray Diffractionresolution 1.65 Å
ligand CA, GLC, GMH, K5B enzyme
Primary referenceStructural definition of hSP-D recognition of Salmonella enterica LPS inner core oligosaccharides reveals alternative binding modes for the same LPS., Littlejohn JR, da Silva RF, Neale WA, Smallcombe CC, Clark HW, Mackay RA, Watson AS, Madsen J, Hood DW, Burns I, Greenhough TJ, Shrive AK, PLoS One. 2018 Jun 18;13(6):e0199175. doi: 10.1371/journal.pone.0199175., eCollection 2018. PMID:29912941
Data retrieval
  • Asymmetric unit, PDB entry: [header only] [complete with coordinates] (90 Kb) [Save to disk]
  • Biological Unit Coordinates (5oxs.pdb1.gz) 83 Kb
  • LPC: Ligand-Protein Contacts for 5OXS
  • CSU: Contacts of Structural Units for 5OXS
  • Structure Factors (2925 Kb)
  • Retrieve 5OXS in mmCIF format [Save to disk]
  • SEQRES to COORDINATES correlation for 5OXS from S2C, [Save to disk]
  • View 5OXS 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 5OXS
  • Ramachandran plot from PDBSum
  • Structure-derived information
  • Dipole moment, from Dipole Server at Weizmann Institute
  • Sequence-derived information
  • View one-letter amino acid or nucleotide sequence for each chain: [5oxs_C] [5oxs_B] [5oxs_A]
  • SWISS-PROT database:
  • Domain organization of by SWISSPFAM
  • Other resources with information on 5OXS
  • Community annotation for 5OXS at PDBWiki (http://pdbwiki.org)

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