8AEJ | pdb_00008aej

X-ray structure of Canis familiaris Odorant Binding Protein 3 bound to menthone

PDB DOI: https://doi.org/10.2210/pdb8AEJ/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Canis lupus familiaris
Expression System: Escherichia coli
Mutation(s): No

Deposited: 2022-07-13 Released: 2023-08-16
Deposition Author(s): Schwartz, M., Briand, L.
Funding Organization(s): Other private

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free:
0.261 (Depositor), 0.260 (DCC)
R-Value Work:
0.220 (Depositor), 0.220 (DCC)
R-Value Observed:
0.222 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.1 of the entry. See complete history.

Literature

Structure of dog odorant binding protein

Glaz, M., Schwartz, M., Briand, L.

To be published.

Macromolecule Content

Total Structure Weight: 21.95 kDa
Atom Count: 1,377
Modeled Residue Count: 160
Deposited Residue Count: 188
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Lipocalin Can f 6.0101	A	188	Canis lupus familiaris	Mutation(s): 0
UniProt
Find proteins for H2B3G5 (Canis lupus familiaris) Explore H2B3G5 Go to UniProtKB: H2B3G5
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	H2B3G5
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
LWE (Subject of Investigation/LOI) Query on LWE Download Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	(+)-menthone C₁₀ H₁₈ O NFLGAXVYCFJBMK-DTWKUNHWSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.84 Å
R-Value Free: 0.261 (Depositor), 0.260 (DCC)
R-Value Work: 0.220 (Depositor), 0.220 (DCC)
R-Value Observed: 0.222 (Depositor)

Space Group: P 3₁ 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 67.075	α = 90
b = 67.075	β = 90
c = 71.985	γ = 120

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
Aimless	data scaling
MOLREP	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-08-16

Deposition Author(s):

Funding Organization	Location	Grant Number
Other private	France	--

Revision History (Full details and data files)

Version 1.0: 2023-08-16
Type: Initial release
Version 1.1: 2024-10-23
Changes: Structure summary

RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729.