5V54

Crystal structure of 5-HT1B receptor in complex with methiothepin

PDB DOI: https://doi.org/10.2210/pdb5V54/pdb

Classification: ELECTRON TRANSPORT
Organism(s): Homo sapiens, Spodoptera frugiperda
Expression System: Spodoptera frugiperda
Mutation(s): Yes
Membrane Protein: Yes OPMPDBTM

Deposited: 2017-03-13 Released: 2018-02-07
Deposition Author(s): Yin, W.C., Zhou, X.E., Yang, D., de Waal, P., Wang, M.T., Dai, A., Cai, X., Huang, C.Y., Liu, P., Yin, Y., Liu, B., Caffrey, M., Melcher, K., Xu, Y., Wang, M.W., Xu, H.E., Jiang, Y.
Funding Organization(s): National Natural Science Foundation, Outstanding Young Scientist Foundation, Jay and Betty Van Andel Foundation, Ministry of Science and Technology of China, National Institutes of Health, Shanghai Science and Technology Development Fund, CAS-Novo Nordisk Research Fund, Youth Innovation Promotion Association of CAS

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.90 Å
R-Value Free:
0.288 (Depositor), 0.288 (DCC)
R-Value Work:
0.272 (Depositor), 0.277 (DCC)
R-Value Observed:
0.273 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

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

Literature

A common antagonistic mechanism for class A GPCRs revealed by the structure of the human 5-HT1B serotonin receptor bound to an antagonist

Yin, W.C., Zhou, X.E., Yang, D., De Waal, P., Wang, M.T., Dai, A., Cai, X., Huang, C.Y., Liu, P., Yin, Y., Liu, B., Caffrey, M., Melcher, K., Xu, Y., Wang, M.W., Xu, H.E., Jiang, Y.

(2018) Cell Discov

Macromolecule Content

Total Structure Weight: 90.64 kDa
Atom Count: 6,180
Modelled Residue Count: 765
Deposited Residue Count: 790
Unique protein chains: 1

Macromolecules

Find similar proteins by:

(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
5-hydroxytryptamine receptor 1B,OB-1 fused 5-HT1b receptor,5-hydroxytryptamine receptor 1B	A, B	395	Homo sapiens, Spodoptera frugiperda	Mutation(s): 1 Gene Names: HTR1B, HTR1DB Membrane Entity: Yes
UniProt & NIH Common Fund Data Resources
Find proteins for P28222 (Homo sapiens) Explore P28222 Go to UniProtKB: P28222
PHAROS: P28222 GTEx: ENSG00000135312
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P28222
Sequence Annotations Expand
Reference Sequence LOADING

Small Molecules

Ligands 1 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
89F Query on 89F Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain D [auth B] MOL2 format, chain C [auth A] MOL2 format, chain D [auth B] mmCIF format, chain C [auth A] mmCIF format, chain D [auth B]	C [auth A], D [auth B]	1-methyl-4-[(5~{S})-3-methylsulfanyl-5,6-dihydrobenzo[b][1]benzothiepin-5-yl]piperazine C₂₀ H₂₄ N₂ S₂ RLJFTICUTYVZDG-SFHVURJKSA-N		Interactions Focus chain C [auth A] Focus chain D [auth B] Interactions & Density Focus chain C [auth A] Focus chain D [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.90 Å
R-Value Free: 0.288 (Depositor), 0.288 (DCC)
R-Value Work: 0.272 (Depositor), 0.277 (DCC)
R-Value Observed: 0.273 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 235.2	α = 90
b = 48.83	β = 124.07
c = 139.22	γ = 90

Software Package:

Software Name	Purpose
PHENIX	refinement
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

View Full Validation Report

Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2018-02-07

Deposition Author(s):

Funding Organization	Location	Grant Number
National Natural Science Foundation	China	31300607
Outstanding Young Scientist Foundation	China	--
Jay and Betty Van Andel Foundation	United States	--
Ministry of Science and Technology of China	China	2012ZX09301001
Ministry of Science and Technology of China	China	2012CB910403
Ministry of Science and Technology of China	China	2013CB9106010
Ministry of Science and Technology of China	China	XDB08020303
Ministry of Science and Technology of China	China	2013ZX09507001
National Institutes of Health	United States	DK071662
National Institutes of Health	United States	GM102545
National Institutes of Health	United States	GM104212
Shanghai Science and Technology Development Fund	China	15DZ2291600
Shanghai Science and Technology Development Fund	China	14431901200
National Natural Science Foundation	China	81373463
CAS-Novo Nordisk Research Fund	China	--
Youth Innovation Promotion Association of CAS	China	--