3IKR

Crystal structure of alpha 1-4 mannobiose bound trimeric human lung surfactant protein D


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.193 

wwPDB Validation 3D Report Full Report


This is version 1.2 of the entry. See complete history

Literature

Structural characterisation of ligand-binding determinants in human lung surfactant protein D: influence of Asp325

Shrive, A.K.Martin, C.Burns, I.Paterson, J.M.Martin, J.D.Townsend, J.P.Waters, P.Clark, H.W.Kishore, U.Reid, K.B.M.Greenhough, T.J.

(2009) J.Mol.Biol. 394: 776-788

  • DOI: 10.1016/j.jmb.2009.09.057
  • Primary Citation of Related Structures:  3IKN, 3IKP, 3IKQ
  • Also Cited By: 4E52

  • PubMed Abstract: 
  • The crystal structures of a biologically and therapeutically active recombinant homotrimeric fragment of human lung surfactant protein D with a series of bound ligands have been determined. While the structures reveal various different binding modes, ...

    The crystal structures of a biologically and therapeutically active recombinant homotrimeric fragment of human lung surfactant protein D with a series of bound ligands have been determined. While the structures reveal various different binding modes, all utilise a similarly positioned pair of mannose-type O3' and O4' hydroxyls with no direct interaction between any non-terminal sugar and protein. The orientation, position, and interactions of the bound terminal sugar depend on the sugar itself, the presence and form of glycosidic linkage, and the environment in the crystal, which, via Asp325, places stereochemical and electronic constraints, different for the three different subunits in the homotrimer, on the ligand-binding site. As a direct consequence of this influence, the other binding-pocket flanking residue, Arg343, exhibits variable conformation and variable interactions with bound ligand and leaves open to question which orientation of terminal mannobiose, and of other terminal disaccharides, may be present in extended physiological ligands. The combined structural evidence shows that there is significant flexibility in recognition; that Asp325, in addition to Arg343, is an important determinant of ligand selectivity, recognition, and binding; and that differences in crystal contact interfaces exert, through Asp325, significant influence on preferred binding modes.


    Related Citations: 
    • High-resolution structural insights into ligand binding and immune cell recognition by human lung surfactant protein D
      Shrive, A.K.,Tharia, H.A.,Strong, P.,Kishore, U.,Burns, I.,Rizkallah, P.J.,Reid, K.B.M.,Greenhough, T.J.
      (2003) J.Mol.Biol. 331: 509


    Organizational Affiliation

    Research Institute of Science and Technology in Medicine, and School of Life Sciences, Keele University, Staffordshire ST5 5BG, UK. a.k.shrive@keele.ac.uk




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Pulmonary surfactant-associated protein D
A, B, C
177Homo sapiensGene Names: SFTPD (COLEC7, PSPD, SFTP4)
Find proteins for P35247 (Homo sapiens)
Go to Gene View: SFTPD
Go to UniProtKB:  P35247
Small Molecules
Ligands 2 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
CA
Query on CA

Download SDF File 
Download CCD File 
A, B, C
CALCIUM ION
Ca
BHPQYMZQTOCNFJ-UHFFFAOYSA-N
 Ligand Interaction
MAN
Query on MAN

Download SDF File 
Download CCD File 
A, B, C
ALPHA-D-MANNOSE
C6 H12 O6
WQZGKKKJIJFFOK-PQMKYFCFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.65 Å
  • R-Value Free: 0.212 
  • R-Value Work: 0.193 
  • Space Group: P 1 21 1
Unit Cell:
Length (Å)Angle (°)
a = 55.520α = 90.00
b = 108.450β = 91.25
c = 55.820γ = 90.00
Software Package:
Software NamePurpose
CNSrefinement
MOSFLMdata reduction
SCALAdata scaling
PDB_EXTRACTdata extraction
ADSCdata collection

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2009-11-17
    Type: Initial release
  • Version 1.1: 2011-07-13
    Type: Version format compliance
  • Version 1.2: 2014-02-19
    Type: Database references