1YAE

Structure of the Kainate Receptor Subunit GluR6 Agonist Binding Domain Complexed with Domoic Acid

PDB DOI: https://doi.org/10.2210/pdb1YAE/pdb

Classification: MEMBRANE PROTEIN
Organism(s): Rattus norvegicus
Expression System: Trichoplusia ni
Mutation(s): No

Deposited: 2004-12-17 Released: 2005-02-01
Deposition Author(s): Nanao, M.H., Green, T., Stern-Bach, Y., Heinemann, S.F., Choe, S.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.334
R-Value Work: 0.275
R-Value Observed: 0.278

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 214.94 kDa
Atom Count: 12,512
Modelled Residue Count: 1,521
Deposited Residue Count: 1,872
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glutamate receptor, ionotropic kainate 2	A, B, C, D, E A, B, C, D, E, F	312	Rattus norvegicus	Mutation(s): 0
UniProt
Find proteins for P42260 (Rattus norvegicus) Explore P42260 Go to UniProtKB: P42260
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P42260
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-L-fucopyranose-(1-6)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	2		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G86851RC GlyCosmos: G86851RC GlyGen: G86851RC

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DOQ Query on DOQ Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain N [auth C] SDF format, chain Q [auth D] SDF format, chain T [auth E] SDF format, chain V [auth F] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain N [auth C] MOL2 format, chain Q [auth D] MOL2 format, chain T [auth E] MOL2 format, chain V [auth F]	H [auth A] K [auth B] N [auth C] Q [auth D] T [auth E] H [auth A], K [auth B], N [auth C], Q [auth D], T [auth E], V [auth F]	(2S,3S,4S)-2-CARBOXY-4-[(1Z,3E,5R)-5-CARBOXY-1-METHYL-1,3-HEXADIENYL]-3-PYRROLIDINEACETIC ACID C₁₅ H₂₁ N O₆ VZFRNCSOCOPNDB-AOKDLOFSSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain V [auth F] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain N [auth C] Focus chain Q [auth D] Focus chain T [auth E] Focus chain V [auth F]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain L [auth C] SDF format, chain M [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain R [auth E] SDF format, chain S [auth E] SDF format, chain U [auth F] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain L [auth C] MOL2 format, chain M [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain R [auth E] MOL2 format, chain S [auth E] MOL2 format, chain U [auth F]	I [auth B] J [auth B] L [auth C] M [auth C] O [auth D] I [auth B], J [auth B], L [auth C], M [auth C], O [auth D], P [auth D], R [auth E], S [auth E], U [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain U [auth F] Interactions & Density Focus chain I [auth B] Focus chain J [auth B] Focus chain L [auth C] Focus chain M [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain R [auth E] Focus chain S [auth E] Focus chain U [auth F]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.11 Å
R-Value Free: 0.334
R-Value Work: 0.275
R-Value Observed: 0.278
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 246.36	α = 90
b = 106.57	β = 133.19
c = 172.69	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
XDS	data reduction
XDS	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2005-02-01

Deposition Author(s):

Revision History (Full details and data files)

Version 1.0: 2005-02-01
Type: Initial release
Version 1.1: 2008-04-30
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2017-08-09
Changes: Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Database references, Derived calculations, Structure summary
Version 2.1: 2023-08-23
Changes: Data collection, Database references, Refinement description, Structure summary

Prepare Data

Validate Data

Deposit Data

Help and Resources

1YAE

Structure of the Kainate Receptor Subunit GluR6 Agonist Binding Domain Complexed with Domoic Acid

Entity ID: 1

UniProt

Entity Groups

Sequence Annotations

Expand

Entity ID: 2

Glycosylation Resources

Experimental Data

Structure Validation

Ligand Structure Quality Assessment

Deposition Data

Revision History (Full details and data files)