5TIO

Crystal Structure of Human Glycine Receptor alpha-3 Bound to AM-3607

PDB DOI: https://doi.org/10.2210/pdb5TIO/pdb

Classification: TRANSPORT PROTEIN
Organism(s): Homo sapiens
Expression System: Spodoptera frugiperda
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2016-10-03 Released: 2017-01-18
Deposition Author(s): Shaffer, P.L., Huang, X., Chen, H.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.254
R-Value Work: 0.233
R-Value Observed: 0.234

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

Literature

Crystal Structures of Human GlyRa3 Bound to a Novel Class of Potentiators with Efficacy in a Mouse Model of Neuropathic Pain

Huang, X., Shaffer, P.L., Ayube, S., Bregman, H., Chen, H., Lehto, S.G., Luther, J.A., Matson, D.J., McDonough, S.I., Michelsen, K., Plant, M.M., Schneider, S., Simard, J.R., Teffera, Y., Yi, S., Zhang, M., DiMauro, E.F., Gingras, J.

To be published.

Macromolecule Content

Total Structure Weight: 212.22 kDa
Atom Count: 13,727
Modelled Residue Count: 1,700
Deposited Residue Count: 1,810
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Glycine receptor subunit alpha-3	A [auth C], B [auth A], C [auth B], D, E	362	Homo sapiens	Mutation(s): 0 Gene Names: GLRA3 Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for O75311 (Homo sapiens) Explore O75311 Go to UniProtKB: O75311
PHAROS: O75311 GTEx: ENSG00000145451
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	O75311
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A [auth C]	Go to GlyGen: O75311-1
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
7C6 Query on 7C6 Download Ideal Coordinates CCD File SDF format, chain F [auth C] SDF format, chain J [auth A] SDF format, chain M [auth B] SDF format, chain P [auth D] SDF format, chain S [auth E] MOL2 format, chain F [auth C] MOL2 format, chain J [auth A] MOL2 format, chain M [auth B] MOL2 format, chain P [auth D] MOL2 format, chain S [auth E] mmCIF format, chain F [auth C] mmCIF format, chain J [auth A] mmCIF format, chain M [auth B] mmCIF format, chain P [auth D] mmCIF format, chain S [auth E]	F [auth C], J [auth A], M [auth B], P [auth D], S [auth E]	(3S,3aS,9bS)-2-[(2H-1,3-benzodioxol-5-yl)sulfonyl]-3,5-dimethyl-1,2,3,3a,5,9b-hexahydro-4H-pyrrolo[3,4-c][1,6]naphthyridin-4-one C₁₉ H₁₉ N₃ O₅ S MXNQASHPCAMJHG-UCMVZMLTSA-N		Interactions Focus chain F [auth C] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth D] Focus chain S [auth E] Interactions & Density Focus chain F [auth C] Focus chain J [auth A] Focus chain M [auth B] Focus chain P [auth D] Focus chain S [auth E]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain I [auth C] MOL2 format, chain I [auth C] mmCIF format, chain I [auth C]	I [auth C]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain I [auth C] Interactions & Density Focus chain I [auth C]
GLY Query on GLY Download Ideal Coordinates CCD File SDF format, chain G [auth C] SDF format, chain K [auth A] SDF format, chain N [auth B] SDF format, chain R [auth D] SDF format, chain T [auth E] MOL2 format, chain G [auth C] MOL2 format, chain K [auth A] MOL2 format, chain N [auth B] MOL2 format, chain R [auth D] MOL2 format, chain T [auth E] mmCIF format, chain G [auth C] mmCIF format, chain K [auth A] mmCIF format, chain N [auth B] mmCIF format, chain R [auth D] mmCIF format, chain T [auth E]	G [auth C], K [auth A], N [auth B], R [auth D], T [auth E]	GLYCINE C₂ H₅ N O₂ DHMQDGOQFOQNFH-UHFFFAOYSA-N		Interactions Focus chain G [auth C] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain T [auth E] Interactions & Density Focus chain G [auth C] Focus chain K [auth A] Focus chain N [auth B] Focus chain R [auth D] Focus chain T [auth E]
ZN Query on ZN Download Ideal Coordinates CCD File SDF format, chain H [auth C] SDF format, chain L [auth A] SDF format, chain O [auth B] SDF format, chain Q [auth D] SDF format, chain U [auth E] MOL2 format, chain H [auth C] MOL2 format, chain L [auth A] MOL2 format, chain O [auth B] MOL2 format, chain Q [auth D] MOL2 format, chain U [auth E] mmCIF format, chain H [auth C] mmCIF format, chain L [auth A] mmCIF format, chain O [auth B] mmCIF format, chain Q [auth D] mmCIF format, chain U [auth E]	H [auth C], L [auth A], O [auth B], Q [auth D], U [auth E]	ZINC ION Zn PTFCDOFLOPIGGS-UHFFFAOYSA-N		Interactions Focus chain H [auth C] Focus chain L [auth A] Focus chain O [auth B] Focus chain Q [auth D] Focus chain U [auth E] Interactions & Density Focus chain H [auth C] Focus chain L [auth A] Focus chain O [auth B] Focus chain Q [auth D] Focus chain U [auth E]

Binding Affinity Annotations
ID	Source	Binding Affinity
7C6	BindingDB: 5TIO	Kd: 11 (nM) from 1 assay(s)
7C6	BindingDB: 5TIO	EC50: min: 16, max: 50 (nM) from 3 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.25 Å
R-Value Free: 0.254
R-Value Work: 0.233
R-Value Observed: 0.234
Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 119.12	α = 90
b = 119.12	β = 90
c = 429.968	γ = 90

Software Package:

Software Name	Purpose
REFMAC	refinement
HKL-2000	data scaling
PDB_EXTRACT	data extraction
PHASER	phasing

Structure Validation

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2017-01-18

Deposition Author(s):

Shaffer, P.L.

Huang, X.

Chen, H.

Revision History (Full details and data files)

Version 1.0: 2017-01-18
Type: Initial release
Version 1.1: 2017-11-22
Changes: Refinement description
Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary
Version 1.3: 2023-10-04
Changes: Data collection, Database references, Refinement description, Structure summary
Version 1.4: 2024-11-20
Changes: Structure summary