1FY3

[G175Q]HBP, A mutant of human heparin binding protein (CAP37)


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.182 

wwPDB Validation   3D Report Full Report



Literature

Two mutants of human heparin binding protein (CAP37): toward the understanding of the nature of lipid A/LPS and BPTI binding.

Kastrup, J.S.Linde, V.Pedersen, A.K.Stoffer, B.Iversen, L.F.Larsen, I.K.Rasmussen, P.B.Flodgaard, H.J.Bjorn, S.E.

(2001) Proteins 42: 442-451

  • DOI: 10.1002/1097-0134(20010301)42:4<442::aid-prot30>3.0.co;2-s
  • Primary Citation of Related Structures:  
    1FY3, 1FY1

  • PubMed Abstract: 
  • Heparin binding protein (HBP) is an inactive serine protease homologue with important implications in host defense during infections and inflammations. Two mutants of human HBP, [R23S,F25E]HBP and [G175Q]HBP, have been produced to investigate structu ...

    Heparin binding protein (HBP) is an inactive serine protease homologue with important implications in host defense during infections and inflammations. Two mutants of human HBP, [R23S,F25E]HBP and [G175Q]HBP, have been produced to investigate structure-function relationships of residues in the putative lipid A/lipopolysaccharide (LPS) binding site and BPTI (bovine pancreatic trypsin inhibitor) binding site. The X-ray structures have been determined at 1.9 A resolution for [G175Q]HBP and at 2.5 A resolution for the [R23S,F25E]HBP mutant, and the structures have been fully refined to R-factors of 18.2 % and 20.7 %, respectively. The G175Q mutation does not alter the overall structure of the protein, but the ability to bind BPTI has been eliminated, and the mutant mediates only a limited stimulation of the LPS-induced cytokine release from human monocytes. The lipid A/LPS binding property of [G175Q]HBP is comparable with that of native HBP. The R23S,F25E mutations do not affect the binding of lipid A/LPS and BPTI or the LPS-induced cytokine release from human monocytes. This shows that two diverse ligands, lipid A/LPS and BPTI, do not share binding sites. Previously, there was convincing evidence for the proposed lipid A/LPS binding site of HBP. Unexpectedly, the extensive structural changes introduced by mutation of Arg23 and Phe25 do not affect the binding of lipid A/LPS, indicating that another not yet identified site on HBP is involved in the binding of lipid A/LPS.


    Related Citations: 
    • Atomic resolution structure of human HBP/CAP37/Azurocidin
      Karlsen, S., Iversen, L.F., Larsen, I.K., Flodgaard, H.J., Kastrup, J.S.
      (1998) Acta Crystallogr D Biol Crystallogr 54: 598
    • Structure of HBP, a multifunctional protein with a serine proteinase fold
      Iversen, L.F., Kastrup, J.S., Bjorn, S.E., Rasmussen, P.B., Wiberg, F.C., Flodgaard, H.J., Larsen, I.K.
      (1997) Nat Struct Biol 4: 265
    • Crystallization and Molecular Replacement Solution of Human Heparin Binding Protein
      Iversen, L.F., Kastrup, J.S., Larsen, I.K., Bjorn, S.E., Rasmussen, P.B., Wiberg, F.C., Flodgaard, H.J.
      (1996) Acta Crystallogr D Biol Crystallogr 52: 1222
    • Structure and function of the N-linked glycans of HBP/CAP37/azurocidin: Crystal structure determination and biological characterization of nonglycosylated HBP
      Iversen, L.F., Kastrup, J.S., Bjorn, S.E., Wiberg, F.C., Larsen, I.K., Flodgaard, H.J., Rasmussen, P.B.
      (1999) Protein Sci 8: 2019

    Organizational Affiliation

    Department of Medicinal Chemistry, Royal Danish School of Pharmacy, Copenhagen, Denmark. kastrup@medchem.dfh.dk



Macromolecules
Find similar proteins by:  (by identity cutoff)  |  Structure
Entity ID: 1
MoleculeChainsSequence LengthOrganismDetailsImage
HEPARIN-BINDING PROTEINA225Homo sapiensMutation(s): 1 
Gene Names: AZU1
Find proteins for P20160 (Homo sapiens)
Explore P20160 
Go to UniProtKB:  P20160
NIH Common Fund Data Resources
PHAROS  P20160
Protein Feature View
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChainsChain Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2 N-Glycosylation Oligosaccharides Interaction
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG

Download Ideal Coordinates CCD File 
A
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
 Ligand Interaction
EOH
Query on EOH

Download Ideal Coordinates CCD File 
A
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
 Ligand Interaction
CL
Query on CL

Download Ideal Coordinates CCD File 
A
CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free: 0.252 
  • R-Value Work: 0.182 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.003α = 90
b = 65.138β = 90
c = 100.655γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
TNTrefinement
TNTphasing

Structure Validation

View Full Validation Report



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2001-09-28
    Type: Initial release
  • Version 1.1: 2008-04-27
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 1.3: 2018-03-07
    Changes: Data collection
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary