8GC4

Domoate-bound GluK2 kainate receptor in partially-open conformation 3

PDB DOI: https://doi.org/10.2210/pdb8GC4/pdb
EM Map EMD-29928: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Rattus norvegicus
Expression System: Spodoptera frugiperda
Mutation(s): No

Deposited: 2023-03-01 Released: 2024-03-13
Deposition Author(s): Bogdanovic, N., Tajima, N.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.93 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.0 of the entry. See complete history.

Literature

Structural basis for kainate receptor activation by a partial agonist

Bogdanovic, N., Tajima, N.

To be published.

Macromolecule Content

Total Structure Weight: 404.26 kDa
Atom Count: 24,135
Modelled Residue Count: 2,968
Deposited Residue Count: 3,500
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	875	Rattus norvegicus	Mutation(s): 0 Gene Names: Grik2, Glur6
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

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	4		N-Glycosylation	Interactions Focus chain E Interactions & Density Focus chain E
Glycosylation Resources
GlyTouCan: G22573RC GlyCosmos: G22573RC GlyGen: G22573RC

Entity ID: 3
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, J	2		N-Glycosylation	Interactions Focus chain F Focus chain J Interactions & Density Focus chain F Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G, H, I, K, L	5		N-Glycosylation	Interactions Focus chain G Focus chain H Focus chain I Focus chain K Focus chain L Interactions & Density Focus chain G Focus chain H Focus chain I Focus chain K Focus chain L
Glycosylation Resources
GlyTouCan: G22768VO GlyCosmos: G22768VO GlyGen: G22768VO

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
DOQ (Subject of Investigation/LOI) Query on DOQ Download Ideal Coordinates CCD File SDF format, chain N [auth A] SDF format, chain Q [auth B] SDF format, chain S [auth C] SDF format, chain V [auth D] MOL2 format, chain N [auth A] MOL2 format, chain Q [auth B] MOL2 format, chain S [auth C] MOL2 format, chain V [auth D]	N [auth A], Q [auth B], S [auth C], V [auth D]	(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 N [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain V [auth D] Interactions & Density Focus chain N [auth A] Focus chain Q [auth B] Focus chain S [auth C] Focus chain V [auth D]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain O [auth B] SDF format, chain P [auth B] SDF format, chain R [auth C] SDF format, chain T [auth D] SDF format, chain U [auth D] MOL2 format, chain M [auth A] MOL2 format, chain O [auth B] MOL2 format, chain P [auth B] MOL2 format, chain R [auth C] MOL2 format, chain T [auth D] MOL2 format, chain U [auth D]	M [auth A] O [auth B] P [auth B] R [auth C] T [auth D] M [auth A], O [auth B], P [auth B], R [auth C], T [auth D], U [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D] Interactions & Density Focus chain M [auth A] Focus chain O [auth B] Focus chain P [auth B] Focus chain R [auth C] Focus chain T [auth D] Focus chain U [auth D]