6DG8

Deposited: 2018-05-17 Released: 2018-11-07
Deposition Author(s): Basak, S., Chakrapani, S.
Funding Organization(s): National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS), American Heart Association

Experimental Data Snapshot

wwPDB Validation 3D Report Full Report

This is version 2.0 of the entry. See complete history.

Macromolecule Content

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 3A	A, B, C, D, E	455	Mus musculus	Mutation(s): 0 Gene Names: Htr3a Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P23979 (Mus musculus) Explore P23979 Go to UniProtKB: P23979
IMPC: MGI:96282
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P23979
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

Entity ID: 2
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, H, J, K, M F, H, J, K, M, N, P, Q, S, T	2		N-Glycosylation	Interactions Focus chain F Focus chain H Focus chain J Focus chain K Focus chain M Focus chain N Focus chain P Focus chain Q Focus chain S Focus chain T Interactions & Density Focus chain F Focus chain H Focus chain J Focus chain K Focus chain M Focus chain N Focus chain P Focus chain Q Focus chain S Focus chain T
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

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

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
SRO Query on SRO Download Ideal Coordinates CCD File SDF format, chain U [auth A] SDF format, chain V [auth B] SDF format, chain W [auth B] SDF format, chain X [auth D] SDF format, chain Y [auth E] MOL2 format, chain U [auth A] MOL2 format, chain V [auth B] MOL2 format, chain W [auth B] MOL2 format, chain X [auth D] MOL2 format, chain Y [auth E]	U [auth A], V [auth B], W [auth B], X [auth D], Y [auth E]	SEROTONIN C₁₀ H₁₂ N₂ O QZAYGJVTTNCVMB-UHFFFAOYSA-N		Interactions Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth D] Focus chain Y [auth E] Interactions & Density Focus chain U [auth A] Focus chain V [auth B] Focus chain W [auth B] Focus chain X [auth D] Focus chain Y [auth E]

Binding Affinity Annotations
ID	Source	Binding Affinity
SRO	BindingDB: 6DG8	Ki: min: 66, max: 1.00e+4 (nM) from 10 assay(s)
		IC50: 727 (nM) from 1 assay(s)
		EC50: min: 141, max: 1.20e+4 (nM) from 5 assay(s)

Experimental Data & Validation

EM Software:

Task	Software Package	Version
RECONSTRUCTION	RELION	2.1
MODEL REFINEMENT	PHENIX	1.13-2998

Entry History & Funding Information

Deposition Author(s):

Basak, S.

Funding Organization	Location	Grant Number
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	1R01GM108921
National Institutes of Health/National Institute of General Medical Sciences (NIH/NIGMS)	United States	3R01GM108921-03S1
American Heart Association	United States	17POST33671152

Version 1.0: 2018-11-07
Type: Initial release
Version 1.1: 2018-11-21
Changes: Data collection, Database references
Version 1.2: 2020-01-08
Changes: Author supporting evidence
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Advisory, Atomic model, Data collection, Derived calculations, Structure summary