5BKG

Cyro-EM structure of human Glycine Receptor alpha2-beta heteromer, glycine bound, (semi)open state

PDB DOI: https://doi.org/10.2210/pdb5BKG/pdb
EM Map EMD-9404: EMDB EMDataResource

Classification: MEMBRANE PROTEIN, SIGNALING PROTEIN
Organism(s): Homo sapiens, Aequorea victoria
Expression System: Homo sapiens
Mutation(s): No
Membrane Protein: Yes OPMPDBTMMemProtMD

Deposited: 2021-03-19 Released: 2021-09-08
Deposition Author(s): Yu, H., Wang, W.
Funding Organization(s): Welch Foundation

Experimental Data Snapshot

Method: ELECTRON MICROSCOPY
Resolution: 3.80 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.

Macromolecule Content

Total Structure Weight: 247.69 kDa
Atom Count: 13,509
Modelled Residue Count: 1,686
Deposited Residue Count: 2,158
Unique protein chains: 2

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor subunit alpha-2	A, B, C, D	364	Homo sapiens	Mutation(s): 0 Gene Names: GLRA2 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P23416 (Homo sapiens) Explore P23416 Go to UniProtKB: P23416
PHAROS: P23416 GTEx: ENSG00000101958
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23416
Sequence Annotations Expand
Reference Sequence

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor subunit beta,Green fluorescent protein	E	702	Homo sapiens, Aequorea victoria	Mutation(s): 0 Gene Names: GLRB, GFP Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P42212 (Aequorea victoria) Explore P42212 Go to UniProtKB: P42212
Find proteins for P48167 (Homo sapiens) Explore P48167 Go to UniProtKB: P48167
PHAROS: P48167 GTEx: ENSG00000109738
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Groups	P42212P48167
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain G [auth A] SDF format, chain I [auth B] SDF format, chain J [auth B] SDF format, chain M [auth C] SDF format, chain N [auth C] SDF format, chain O [auth D] SDF format, chain P [auth D] SDF format, chain Q [auth E] MOL2 format, chain F [auth A] MOL2 format, chain G [auth A] MOL2 format, chain I [auth B] MOL2 format, chain J [auth B] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] MOL2 format, chain O [auth D] MOL2 format, chain P [auth D] MOL2 format, chain Q [auth E]	F [auth A] G [auth A] I [auth B] J [auth B] M [auth C] F [auth A], G [auth A], I [auth B], J [auth B], M [auth C], N [auth C], O [auth D], P [auth D], Q [auth E]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E] Interactions & Density Focus chain F [auth A] Focus chain G [auth A] Focus chain I [auth B] Focus chain J [auth B] Focus chain M [auth C] Focus chain N [auth C] Focus chain O [auth D] Focus chain P [auth D] Focus chain Q [auth E]
GLY (Subject of Investigation/LOI) Query on GLY Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain K [auth B] SDF format, chain L [auth B] MOL2 format, chain H [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth B]	H [auth A], K [auth B], L [auth B]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B] Interactions & Density Focus chain H [auth A] Focus chain K [auth B] Focus chain L [auth B]