4HFO | pdb_00004hfo

Biogenic amine-binding protein selenomethionine derivative

Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free: 
    0.349 (Depositor), 0.335 (DCC) 
  • R-Value Work: 
    0.321 (Depositor) 
  • R-Value Observed: 
    0.323 (Depositor) 

wwPDB Validation 3D Report Full Report

Validation slider image for 4HFO

This is version 1.3 of the entry. See complete history. 

Literature

Structure and ligand-binding properties of the biogenic amine-binding protein from the saliva of a blood-feeding insect vector of Trypanosoma cruzi.

Xu, X., Chang, B.W., Mans, B.J., Ribeiro, J.M., Andersen, J.F.

(2013) Acta Crystallogr D Biol Crystallogr 69: 105-113

  • DOI: https://doi.org/10.1107/S0907444912043326
  • Primary Citation Related Structures: 
    4GE1, 4GET, 4HFO

  • PubMed Abstract: 

    Proteins that bind small-molecule mediators of inflammation and hemostasis are essential for blood-feeding by arthropod vectors of infectious disease. In ticks and triatomine insects, the lipocalin protein family is greatly expanded and members have been shown to bind biogenic amines, eicosanoids and ADP. These compounds are potent mediators of platelet activation, inflammation and vascular tone. In this paper, the structure of the amine-binding protein (ABP) from Rhodnius prolixus, a vector of the trypanosome that causes Chagas disease, is described. ABP binds the biogenic amines serotonin and norepinephrine with high affinity. A complex with tryptamine shows the presence of a binding site for a single ligand molecule in the central cavity of the β-barrel structure. The cavity contains significant additional volume, suggesting that this protein may have evolved from the related nitrophorin proteins, which bind a much larger heme ligand in the central cavity.

    • Organizational Affiliation: 
    • Laboratory of Malaria and Vector Research, NIH/NIAID, Rockville, MD 20852, USA.

Macromolecule Content 

  • Total Structure Weight: 177.37 kDa 
  • Atom Count: 12,360 
  • Modeled Residue Count: 1,552 
  • Deposited Residue Count: 1,560 
  • Unique protein chains: 1

Macromolecules

Find similar proteins by:
|  3D Structure
Entity ID: 1
MoleculeChains  Sequence LengthOrganismDetailsImage
Biogenic amine-binding protein195Rhodnius prolixusMutation(s): 0 
UniProt
Find proteins for Q86PT9 (Rhodnius prolixus)
Explore Q86PT9 
Go to UniProtKB:  Q86PT9
Entity Groups
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ86PT9
Sequence Annotations
Expand
Reference Sequence

Small Molecules

Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
MSE
Query on MSE
A
B
C
D
E [auth I]
A,
B,
C,
D,
E [auth I],
F [auth J],
G [auth K],
H [auth L]
L-PEPTIDE LINKINGC5 H11 N O2 SeMET

Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.00 Å
  • R-Value Free:  0.349 (Depositor), 0.335 (DCC) 
  • R-Value Work:  0.321 (Depositor) 
  • R-Value Observed: 0.323 (Depositor) 
Space Group: P 1 21 1
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 102.164α = 90
b = 70.661β = 99.16
c = 108.413γ = 90
Software Package:
Software NamePurpose
DENZOdata reduction
SCALEPACKdata scaling
PHENIXrefinement
PDB_EXTRACTdata extraction
HKL-3000phasing

Structure Validation

View Full Validation Report



View more in-depth experimental data

Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2013-01-02
    Type: Initial release
  • Version 1.1: 2013-01-23
    Changes: Database references
  • Version 1.2: 2017-11-15
    Changes: Refinement description
  • Version 1.3: 2024-10-16
    Changes: Data collection, Database references, Derived calculations, Structure summary