8GC2 | pdb_00008gc2

Domoate-bound GluK2 kainate receptor in partially-open conformation 1

PDB DOI: https://doi.org/10.2210/pdb8GC2/pdb
EM Map EMD-29926: EMDB EMDataResource

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

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: 4.10 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

This is version 1.1 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: 404.55 kDa
Atom Count: 24,342
Modeled Residue Count: 2,993
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 Membrane Entity: Yes
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
Glycosylation
Glycosylation Sites: 3	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D	Go to GlyGen: P42260-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
alpha-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E, L	5		N-Glycosylation	Interactions Focus chain E Focus chain L Interactions & Density Focus chain E Focus chain L
Glycosylation Resources
GlyTouCan: G21381MC GlyCosmos: G21381MC GlyGen: G21381MC

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
beta-D-mannopyranose-(1-3)-[alpha-D-mannopyranose-(1-6)]alpha-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	G	5		N-Glycosylation	Interactions Focus chain G Interactions & Density Focus chain G
Glycosylation Resources
GlyTouCan: G66753FB GlyCosmos: G66753FB GlyGen: G66753FB

Entity ID: 5
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	H, I, K	5		N-Glycosylation	Interactions Focus chain H Focus chain I Focus chain K Interactions & Density Focus chain H Focus chain I Focus chain K
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 O [auth A] SDF format, chain R [auth B] SDF format, chain U [auth C] MOL2 format, chain O [auth A] MOL2 format, chain R [auth B] MOL2 format, chain U [auth C] mmCIF format, chain O [auth A] mmCIF format, chain R [auth B] mmCIF format, chain U [auth C]	O [auth A], R [auth B], U [auth C]	(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 O [auth A] Focus chain R [auth B] Focus chain U [auth C] Interactions & Density Focus chain O [auth A] Focus chain R [auth B] Focus chain U [auth C]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth A] SDF format, chain N [auth A] SDF format, chain P [auth B] SDF format, chain Q [auth B] SDF format, chain V [auth D] SDF format, chain W [auth D] SDF format, chain T [auth C] SDF format, chain S [auth C] MOL2 format, chain M [auth A] MOL2 format, chain N [auth A] MOL2 format, chain P [auth B] MOL2 format, chain Q [auth B] MOL2 format, chain V [auth D] MOL2 format, chain W [auth D] MOL2 format, chain T [auth C] MOL2 format, chain S [auth C] mmCIF format, chain M [auth A] mmCIF format, chain N [auth A] mmCIF format, chain P [auth B] mmCIF format, chain Q [auth B] mmCIF format, chain V [auth D] mmCIF format, chain W [auth D] mmCIF format, chain T [auth C] mmCIF format, chain S [auth C]	M [auth A] N [auth A] P [auth B] Q [auth B] S [auth C] M [auth A], N [auth A], P [auth B], Q [auth B], S [auth C], T [auth C], V [auth D], W [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D] Interactions & Density Focus chain M [auth A] Focus chain N [auth A] Focus chain P [auth B] Focus chain Q [auth B] Focus chain S [auth C] Focus chain T [auth C] Focus chain V [auth D] Focus chain W [auth D]