7U2M | pdb_00007u2m

A novel compound mimics the structural and functional effects of the full agonist glycine on glycine channels-desenstized state

PDB DOI: https://doi.org/10.2210/pdb7U2M/pdb
EM Map EMD-26315: EMDB EMDataResource

Classification: MEMBRANE PROTEIN
Organism(s): Danio rerio
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes OPM PDBTM MemProtMD

Deposited: 2022-02-24 Released: 2023-03-08
Deposition Author(s): Zhu, H., Gouaux, E.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

wwPDB Validation 3D Report Full Report

Validation slider image for 7U2M

This is version 1.1 of the entry. See complete history.

Literature

A novel compound mimics the structural and functional effects of the full agonist glycine on glycine channels-desenstized state

Zhu, H., Gouaux, E.

To be published.

Macromolecule Content

Total Structure Weight: 266.18 kDa
Atom Count: 14,155
Modeled Residue Count: 1,730
Deposited Residue Count: 2,290
Unique protein chains: 1

Macromolecules

Find similar proteins by:

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor subunit alphaZ1	A, B, C, D, E	458	Danio rerio	Mutation(s): 0 Gene Names: glra1 Membrane Entity: Yes
UniProt
Find proteins for O93430 (Danio rerio) Explore O93430 Go to UniProtKB: O93430
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	O93430
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	F, G, H, I, J	3		N-Glycosylation	Interactions Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J Interactions & Density Focus chain F Focus chain G Focus chain H Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G15407YE GlyCosmos: G15407YE GlyGen: G15407YE

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
L2L (Subject of Investigation/LOI) Query on L2L Download:Ideal Coordinates CCD File SDF format, chain O [auth E] SDF format, chain N [auth D] SDF format, chain M [auth C] SDF format, chain L [auth B] SDF format, chain K [auth A] MOL2 format, chain O [auth E] MOL2 format, chain N [auth D] MOL2 format, chain M [auth C] MOL2 format, chain L [auth B] MOL2 format, chain K [auth A] mmCIF format, chain O [auth E] mmCIF format, chain N [auth D] mmCIF format, chain M [auth C] mmCIF format, chain L [auth B] mmCIF format, chain K [auth A]	K [auth A], L [auth B], M [auth C], N [auth D], O [auth E]	aminomethanesulfonic acid C H₅ N O₃ S OBESRABRARNZJB-UHFFFAOYSA-N		Interactions Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E] Interactions & Density Focus chain K [auth A] Focus chain L [auth B] Focus chain M [auth C] Focus chain N [auth D] Focus chain O [auth E]

Experimental Data & Validation

Experimental Data

Method: ELECTRON MICROSCOPY
Resolution: 2.90 Å
Aggregation State: PARTICLE
Reconstruction Method: SINGLE PARTICLE

Structure Validation

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-03-08

Deposition Author(s):

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	R01 GM100400

Revision History (Full details and data files)

Version 1.0: 2023-03-08
Type: Initial release
Version 1.1: 2024-11-06
Changes: Data collection, Structure summary

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RCSB PDB Core Operations are funded by the U.S. National Science Foundation (DBI-2321666), the US Department of Energy (DE-SC0019749), and the National Cancer Institute, National Institute of Allergy and Infectious Diseases, and National Institute of General Medical Sciences of the National Institutes of Health under grant R01GM157729. RCSB PDB uses resources of the National Energy Research Scientific Computing Center (NERSC), a Department of Energy User Facility.