4RUN | pdb_00004run

Crystal structure of human odorant binding protein OBPIIa

• PDB DOI: https://doi.org/10.2210/pdb4RUN/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): Yes 


• Deposited: 2014-11-21 Released: 2015-04-08 
• Deposition Author(s): Schiefner, A., Skerra, A.

---

Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free: 
  0.284 (Depositor), 0.288 (DCC) 
• R-Value Work: 
  0.235 (Depositor), 0.236 (DCC) 
• R-Value Observed: 
  0.237 (Depositor) 

Starting Model: experimental

Literature

Crystal structure of the human odorant binding protein, OBPIIa.

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

(2015) Proteins 83: 1180-1184

• PubMed: 25810031 
• DOI: https://doi.org/10.1002/prot.24797
• Primary Citation Related Structures: 
  4RUN


• 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.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Cyclic - C2  (Explore in 3D)
Global Stoichiometry: Homo 2-mer - A2 

Biological assembly 3 generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 37.5 kDa 
• Atom Count: 2,433 
• Modeled Residue Count: 299 
• Deposited Residue Count: 322 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Odorant-binding protein 2a	A, B	161	Homo sapiens	Mutation(s): 2  Gene Names: OBP2A
UniProt & NIH Common Fund Data Resources
Find proteins for Q9NY56 (Homo sapiens) Explore Q9NY56  Go to UniProtKB:  Q9NY56
PHAROS:  Q9NY56 GTEx:  ENSG00000122136

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
FLC	C [auth A]	CITRATE ANION C6 H5 O7 KRKNYBCHXYNGOX-UHFFFAOYSA-K

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.60 Å
• R-Value Free:  0.284 (Depositor), 0.288 (DCC) 
• R-Value Work:  0.235 (Depositor), 0.236 (DCC) 
• R-Value Observed: 0.237 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 52.949	α = 90
b = 52.949	β = 90
c = 232.098	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
MAR345	data collection
XDS	data reduction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-04-08 
Deposition Author(s): Schiefner, A., Skerra, A.

Revision History  

• 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
• Version 1.4: 2024-11-27
  Changes: Structure summary