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 (Depositor) 
  • R-Value Work: 
    0.182 (Depositor), 0.180 (DCC) 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.2 of the entry. See complete history


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

  • 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 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.


  • 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)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEPARIN-BINDING PROTEIN225Homo sapiensMutation(s): 1 
UniProt & NIH Common Fund Data Resources
Find proteins for P20160 (Homo sapiens)
Explore P20160 
Go to UniProtKB:  P20160
PHAROS:  P20160
GTEx:  ENSG00000172232 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupP20160
Glycosylation
Glycosylation Sites: 2Go to GlyGen: P20160-1
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

Help

Entity ID: 2
MoleculeChains Length2D Diagram Glycosylation3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
B
2N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT
GlyCosmos:  G42666HT
GlyGen:  G42666HT
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.89 Å
  • R-Value Free:  0.252 (Depositor) 
  • R-Value Work:  0.182 (Depositor), 0.180 (DCC) 
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

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Ligand Structure Quality Assessment 


Entry History 

Deposition Data

Revision History  (Full details and data files)

  • 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
  • Version 2.1: 2021-11-03
    Changes: Database references, Structure summary
  • Version 2.2: 2024-11-20
    Changes: Data collection, Structure summary