6PS8

XFEL MT1R structure by ligand exchange from agomelatine to 2-phenylmelatonin.


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.259 

wwPDB Validation 3D Report Full Report


This is version 1.0 of the entry. See complete history

Literature

Toward G protein-coupled receptor structure-based drug design using X-ray lasers

Ishchenko, A.Stauch, B.Han, G.W.Batyuk, A.Shiriaeva, A.Li, C.Zatsepin, N.A.Weierstall, U.Liu, W.Nango, E.Nakane, T.Tanaka, R.Tono, K.Joti, Y.Iwata, S.Moraes, I.Gati, C.Cherezov, V.

(2019) Iucrj 6: 1106-1119


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Fusion protein of Melatonin receptor type 1A and GlgA glycogen synthase
A
503Pyrococcus abyssi (strain GE5 / Orsay)Homo sapiens
This entity is chimeric
Mutation(s): 9 
Gene Names: MTNR1A
Membrane protein
mpstruc
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
MT1 melatonin receptor with bound ramelteon
Find proteins for Q9V2J8 (Pyrococcus abyssi (strain GE5 / Orsay))
Go to UniProtKB:  Q9V2J8
Find proteins for P48039 (Homo sapiens)
Go to Gene View: MTNR1A
Go to UniProtKB:  P48039
Small Molecules
Ligands 1 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
JEY
Query on JEY

Download SDF File 
Download CCD File 
A
N-[2-(5-methoxy-2-phenyl-1H-indol-3-yl)ethyl]acetamide
2-phenylmelatonin
C19 H20 N2 O2
OFCLARYYBGKCHN-UHFFFAOYSA-N
 Ligand Interaction
Modified Residues  1 Unique
IDChainsTypeFormula2D DiagramParent
YCM
Query on YCM
A
L-PEPTIDE LINKINGC5 H10 N2 O3 SCYS
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.3 Å
  • R-Value Free: 0.307 
  • R-Value Work: 0.259 
  • Space Group: P 4 21 2
Unit Cell:
Length (Å)Angle (°)
a = 122.200α = 90.00
b = 122.200β = 90.00
c = 122.600γ = 90.00
Software Package:
Software NamePurpose
REFMACrefinement
PDB_EXTRACTdata extraction
PHASERphasing
CrystFELdata scaling
CrystFELdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
National Institutes of Health/National Institute of General Medical SciencesUnited StatesR35 GM127086

Revision History 

  • Version 1.0: 2019-11-13
    Type: Initial release