3FVO

Crystal structure of the human glutamate receptor, GluR5, ligand-binding core in complex with 8-epi-neodysiherbaine A in space group P1

• PDB DOI: https://doi.org/10.2210/pdb3FVO/pdb

• Classification: MEMBRANE PROTEIN
• Organism(s): Homo sapiens
• Expression System: Escherichia coli
• Mutation(s): No 


• Deposited: 2009-01-16 Released: 2010-01-19 
• Deposition Author(s): Unno, M., Sasaki, M., Ikeda-Saito, M.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.191 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 

Literature

Crystal Structures of Human GluR5 Ligand-Binding Core in Complexes with Novel Marine-Derived Toxins, Dysiherbaine and Neodysiherbaine A, and Their Analogues

Unno, M., Shinohara, M., Takayama, K., Teruya, K., Doh-ura, K., Sakai, R., Sasaki, M., Ikeda-Saito, M.

To be published.

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: 60.07 kDa 
• Atom Count: 4,835 
• Modelled Residue Count: 512 
• Deposited Residue Count: 512 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor, ionotropic kainate 1	A, B	256	Homo sapiens	Mutation(s): 0
UniProt & NIH Common Fund Data Resources
Find proteins for P39086 (Homo sapiens) Explore P39086  Go to UniProtKB:  P39086
PHAROS:  P39086 GTEx:  ENSG00000171189

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
8EP	G [auth A], P [auth B]	(2R,3aR,6R,7S,7aR)-2-[(2S)-2-amino-3-hydroxy-3-oxo-propyl]-6,7-dihydroxy-3,3a,5,6,7,7a-hexahydrofuro[4,5-b]pyran-2-carboxylic acid C11 H17 N O8 NRTJEXLNSCGBJU-JROTZIKASA-N
SO4	H [auth A], I [auth A], Q [auth B], R [auth B]	SULFATE ION O4 S QAOWNCQODCNURD-UHFFFAOYSA-L
GOL	C [auth A], D [auth A], E [auth A], F [auth A], J [auth B], K [auth B], L [auth B], M [auth B], N [auth B], O [auth B]	GLYCEROL C3 H8 O3 PEDCQBHIVMGVHV-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.50 Å
• R-Value Free: 0.191 
• R-Value Work: 0.165 
• R-Value Observed: 0.166 
• Space Group: P 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 47.717	α = 94.19
b = 50.756	β = 95.9
c = 63.29	γ = 117.95

Software Package:

Software Name	Purpose
CNS	refinement
REFMAC	refinement
HKL-2000	data reduction
HKL-2000	data scaling
CNS	phasing

Structure Validation

Entry History 

Deposition Data

• Released Date: 2010-01-19 
Deposition Author(s): Unno, M., Sasaki, M., Ikeda-Saito, M.

Revision History  

• Version 1.0: 2010-01-19
  Type: Initial release
  
• Version 1.1: 2011-07-13
  Changes: Version format compliance
• Version 1.2: 2017-08-16
  Changes: Refinement description, Source and taxonomy
• Version 1.3: 2023-11-01
  Changes: Data collection, Database references, Derived calculations, Refinement description