5CFB

Crystal Structure of Human Glycine Receptor alpha-3 Bound to Strychnine

• PDB DOI: https://doi.org/10.2210/pdb5CFB/pdb

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


• Deposited: 2015-07-08 Released: 2015-09-30 
• Deposition Author(s): Shaffer, P.L., Huang, X., Chen, H.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.04 Å
• R-Value Free: 0.283 
• R-Value Work: 0.260 
• R-Value Observed: 0.262 

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: 212.47 kDa 
• Atom Count: 13,540 
• Modelled Residue Count: 1,684 
• 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,Glycine receptor subunit alpha-3	A, B, C, 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

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
SY9	H [auth A], K [auth B], L [auth C], M [auth D], N [auth E]	STRYCHNINE C21 H22 N2 O2 QMGVPVSNSZLJIA-FVWCLLPLSA-N
NAG	I [auth A], J [auth B], O [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N

Binding Affinity Annotations
ID	Source	Binding Affinity
SY9	BindingDB:  5CFB	Ki: min: 12, max: 123 (nM) from 3 assay(s)
		IC50: min: 51, max: 151 (nM) from 4 assay(s)

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.04 Å
• R-Value Free: 0.283 
• R-Value Work: 0.260 
• R-Value Observed: 0.262 
• Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 140.242	α = 90
b = 143.198	β = 90
c = 180.054	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
SCALEPACK	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2015-09-30 
Deposition Author(s): Shaffer, P.L., Huang, X., Chen, H.

Revision History  

• Version 1.0: 2015-09-30
  Type: Initial release
  
• Version 1.1: 2015-10-14
  Changes: Database references
• Version 1.2: 2015-10-21
  Changes: Database references
• Version 1.3: 2016-07-20
  Changes: Data collection
• Version 1.4: 2017-11-22
  Changes: Derived calculations, Refinement description
• Version 2.0: 2020-07-29
  Type: Remediation
  Reason: Carbohydrate remediation
  Changes: Atomic model, Data collection, Derived calculations, Structure summary
• Version 2.1: 2023-09-27
  Changes: Data collection, Database references, Refinement description, Structure summary