4MR8

Crystal structure of the extracellular domain of human GABA(B) receptor bound to the antagonist CGP35348

• PDB DOI: https://doi.org/10.2210/pdb4MR8/pdb

• Classification: SIGNALING PROTEIN/ANTAGONIST
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  mpstruc


• Deposited: 2013-09-17 Released: 2013-12-11 
• Deposition Author(s): Geng, Y., Bush, M., Mosyak, L., Wang, F., Fan, Q.R.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.223 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Hetero 2-mer - A1B1 Pseudo Symmetry: Cyclic - C2  (Explore in 3D)
Pseudo Stoichiometry: Homo 2-mer - A2 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content

• Total Structure Weight: 98.68 kDa 
• Atom Count: 7,085 
• Modelled Residue Count: 810 
• Deposited Residue Count: 853 
• Unique protein chains: 2

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid type B receptor subunit 1	A	420	Homo sapiens	Mutation(s): 0  Gene Names: GABBR1, GPRC3A Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for Q9UBS5 (Homo sapiens) Explore Q9UBS5  Go to UniProtKB:  Q9UBS5
PHAROS:  Q9UBS5 GTEx:  ENSG00000204681

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Gamma-aminobutyric acid type B receptor subunit 2	B	433	Homo sapiens	Mutation(s): 0  Gene Names: GABBR2, GPR51, GPRC3B Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O75899 (Homo sapiens) Explore O75899  Go to UniProtKB:  O75899
PHAROS:  O75899 GTEx:  ENSG00000136928

Oligosaccharides

Help

Entity ID: 3
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
beta-D-mannopyranose-(1-3)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	C	5		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G51347YJ GlyCosmos:  G51347YJ GlyGen:  G51347YJ

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose	D	3		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G21290RB GlyCosmos:  G21290RB GlyGen:  G21290RB

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
2BW	F [auth A]	(S)-(3-aminopropyl)(diethoxymethyl)phosphinic acid C8 H20 N O4 P QIIVUOWTHWIXFO-UHFFFAOYSA-N
NAG	E [auth A]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
2BW	BindingDB:  4MR8	IC50: min: 2500, max: 2.70e+4 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.15 Å
• R-Value Free: 0.223 
• R-Value Work: 0.209 
• R-Value Observed: 0.210 
• Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.98	α = 90
b = 112.75	β = 97.8
c = 73.45	γ = 90

Software Package:

Software Name	Purpose
SCALA	data scaling
BUSTER-TNT	refinement
PDB_EXTRACT	data extraction
XDS	data scaling
XDS	data reduction
PHASER	phasing
BUSTER	refinement

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-12-11 
Deposition Author(s): Geng, Y., Bush, M., Mosyak, L., Wang, F., Fan, Q.R.

Revision History  

• Version 1.0: 2013-12-11
  Type: Initial release
  
• Version 1.1: 2013-12-18
  Changes: Database references
• Version 1.2: 2014-02-05
  Changes: Database references
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Database references, Derived calculations, Structure summary
• Version 2.1: 2023-09-20
  Changes: Data collection, Database references, Refinement description, Structure summary