1A7S

ATOMIC RESOLUTION STRUCTURE OF HBP

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.189 
  • R-Value Observed: 0.159 

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Literature

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: 598-609

  • DOI: https://doi.org/10.1107/s0907444997016193
  • Primary Citation of Related Structures:  
    1A7S

  • PubMed Abstract: 

    Crystals of human heparin binding protein (HBP) diffract to 1.1 A when flash-frozen at 120 K. The atomic resolution structure has been refined anisotropically using SHELXL96. The final model of HBP consists of 221 amino-acid residues of 225 possible, three glycosylation units, one chloride ion, 15 precipitant ethanol molecules and 323 water molecules. The structure is refined to a final crystallographic R factor of 15.9% and Rfree(5%) of 18.9% using all data. A putative protein kinase C activation site has been identified, involving residues 113-120. The structure is compared to the previously determined 2.3 A resolution structure of HBP.

    • Organizational Affiliation: 

    Department of Medicinal Chemistry, Royal Danish School of Pharmacy, Universitetsparken 2, DK-2100 Copenhagen, Denmark. solveig.karlsen@chem.uit.no


Macromolecules
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(by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
HEPARIN BINDING PROTEIN225Homo sapiensMutation(s): 0 
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
Sequence Annotations
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  • Reference Sequence
Oligosaccharides

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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
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
NAG
Query on NAG
Download Ideal Coordinates CCD File 
C [auth A]2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EOH
Query on EOH
Download Ideal Coordinates CCD File 
E [auth A]
F [auth A]
G [auth A]
H [auth A]
I [auth A]
E [auth A],
F [auth A],
G [auth A],
H [auth A],
I [auth A],
J [auth A],
K [auth A],
L [auth A],
M [auth A],
N [auth A],
O [auth A],
P [auth A],
Q [auth A],
R [auth A],
S [auth A]
ETHANOL
C2 H6 O
LFQSCWFLJHTTHZ-UHFFFAOYSA-N
CL
Query on CL
Download Ideal Coordinates CCD File 
D [auth A]CHLORIDE ION
Cl
VEXZGXHMUGYJMC-UHFFFAOYSA-M
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 1.12 Å
  • R-Value Free: 0.189 
  • R-Value Observed: 0.159 
  • Space Group: P 21 21 21
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 38.22α = 90
b = 65.16β = 90
c = 101.58γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
SHELXL-96model building
SHELXL-96refinement
SHELXL-96phasing

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 1999-03-23
    Type: Initial release
  • Version 1.1: 2008-03-24
    Changes: Version format compliance
  • Version 1.2: 2011-07-13
    Changes: Non-polymer description, Version format compliance
  • Version 2.0: 2020-07-29
    Type: Remediation
    Reason: Carbohydrate remediation
    Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary