Crystal structure of human odorant binding protein OBPIIa

Experimental Data Snapshot

  • Resolution: 2.60 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 

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This is version 1.3 of the entry. See complete history


Crystal structure of the human odorant binding protein, OBPIIa.

Schiefner, A.Freier, R.Eichinger, A.Skerra, A.

(2015) Proteins 83: 1180-1184

  • DOI: https://doi.org/10.1002/prot.24797
  • Primary Citation of Related Structures:  

  • PubMed Abstract: 

    Human odorant-binding protein, OBPIIa , is expressed by nasal epithelia to facilitate transport of hydrophobic odorant molecules across the aqueous mucus. Here, we report its crystallographic analysis at 2.6 Å resolution. OBPIIa is a monomeric protein that exhibits the classical lipocalin fold with a conserved eight-stranded β-barrel harboring a remarkably large hydrophobic pocket. Basic residues within the four loops that shape the entrance to this ligand-binding site evoke a positive electrostatic potential. Human OBPIIa shows distinct features compared with other mammalian OBPs, including a potentially reactive Cys side chain within its pocket similar to human tear lipocalin.

  • Organizational Affiliation

    Munich Center for Integrated Protein Science (CIPS-M) and Lehrstuhl für Biologische Chemie, Technische Universität München, 85350 Freising-Weihenstephan, Germany.

Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
Odorant-binding protein 2a
A, B
161Homo sapiensMutation(s): 2 
Gene Names: OBP2A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NY56 (Homo sapiens)
Explore Q9NY56 
Go to UniProtKB:  Q9NY56
GTEx:  ENSG00000122136 
Entity Groups  
Sequence Clusters30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt GroupQ9NY56
Sequence Annotations
  • Reference Sequence
Small Molecules
Ligands 1 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
Query on FLC

Download Ideal Coordinates CCD File 
C6 H5 O7
Experimental Data & Validation

Experimental Data

  • Resolution: 2.60 Å
  • R-Value Free: 0.284 
  • R-Value Work: 0.235 
  • R-Value Observed: 0.237 
  • Space Group: P 41 21 2
Unit Cell:
Length ( Å )Angle ( ˚ )
a = 52.949α = 90
b = 52.949β = 90
c = 232.098γ = 90
Software Package:
Software NamePurpose
XSCALEdata scaling
PDB_EXTRACTdata extraction
MAR345data collection
XDSdata reduction

Structure Validation

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Entry History 

Deposition Data

Revision History  (Full details and data files)

  • Version 1.0: 2015-04-08
    Type: Initial release
  • Version 1.1: 2015-06-10
    Changes: Database references
  • Version 1.2: 2017-11-22
    Changes: Refinement description
  • Version 1.3: 2023-09-20
    Changes: Data collection, Database references, Derived calculations, Refinement description