5TIO

Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607

• PDB DOI: https://doi.org/10.2210/pdb5TIO/pdb

• Classification: TRANSPORT PROTEIN
• Organism(s): Homo sapiens
• Expression System: Spodoptera frugiperda
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMDmpstruc


• Deposited: 2016-10-03 Released: 2017-01-18 
• Deposition Author(s): Shaffer, P.L., Huang, X., Chen, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.254 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 

Starting Model: experimental

Literature

Crystal Structures of Human GlyRa3 Bound to a Novel Class of Potentiators with Efficacy in a Mouse Model of Neuropathic Pain

Huang, X., Shaffer, P.L., Ayube, S., Bregman, H., Chen, H., Lehto, S.G., Luther, J.A., Matson, D.J., McDonough, S.I., Michelsen, K., Plant, M.M., Schneider, S., Simard, J.R., Teffera, Y., Yi, S., Zhang, M., DiMauro, E.F., Gingras, J.

To be published.

Biological Assembly 1  

Global Symmetry: Cyclic - C5  (Explore in 3D)
Global Stoichiometry: Homo 5-mer - A5 

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

Macromolecule Content

• Total Structure Weight: 212.22 kDa 
• Atom Count: 13,727 
• Modelled Residue Count: 1,700 
• Deposited Residue Count: 1,810 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor subunit alpha-3	A [auth C], B [auth A], C [auth B], D, E	362	Homo sapiens	Mutation(s): 0  Gene Names: GLRA3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O75311 (Homo sapiens) Explore O75311  Go to UniProtKB:  O75311
PHAROS:  O75311 GTEx:  ENSG00000145451
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: O75311-1

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
7C6	F [auth C], J [auth A], M [auth B], P [auth D], S [auth E]	(3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one C19 H19 N3 O5 S MXNQASHPCAMJHG-UCMVZMLTSA-N
NAG	I [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
GLY	G [auth C], K [auth A], N [auth B], R [auth D], T [auth E]	GLYCINE C2 H5 N O2 DHMQDGOQFOQNFH-UHFFFAOYSA-N
ZN	H [auth C], L [auth A], O [auth B], Q [auth D], U [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
7C6	BindingDB:  5TIO	Kd: 11 (nM) from 1 assay(s)
		EC50: min: 16, max: 50 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.25 Å
• R-Value Free: 0.254 
• R-Value Work: 0.233 
• R-Value Observed: 0.234 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.12	α = 90
b = 119.12	β = 90
c = 429.968	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2017-01-18 
Deposition Author(s): Shaffer, P.L., Huang, X., Chen, H.

Revision History  

• Version 1.0: 2017-01-18
  Type: Initial release
  
• Version 1.1: 2017-11-22
  Changes: Refinement description
• Version 1.2: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Data collection, Derived calculations, Structure summary
• Version 1.3: 2023-10-04
  Changes: Data collection, Database references, Refinement description, Structure summary