6IIU

Crystal structure of the human thromboxane A2 receptor bound to ramatroban


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Structural basis for ligand recognition of the human thromboxane A2receptor.

Fan, H.Chen, S.Yuan, X.Han, S.Zhang, H.Xia, W.Xu, Y.Zhao, Q.Wu, B.

(2019) Nat. Chem. Biol. 15: 27-33


Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
Soluble cytochrome b562,Thromboxane A2 receptor,Rubredoxin,Thromboxane A2 receptor
A
484Escherichia coliHomo sapiensClostridium pasteurianum
This entity is chimeric
Mutation(s): 4 
Gene Names: cybC, TBXA2R,
Membrane protein
mpstruct
Group: 
TRANSMEMBRANE PROTEINS: ALPHA-HELICAL
Sub Group: 
G Protein-Coupled Receptors (GPCRs)
Protein: 
thromboxane A2 receptor with bound ramatroban
Find proteins for P0ABE7 (Escherichia coli)
Go to UniProtKB:  P0ABE7
Find proteins for P21731 (Homo sapiens)
Go to Gene View: TBXA2R
Go to UniProtKB:  P21731
Find proteins for P00268 (Clostridium pasteurianum)
Go to UniProtKB:  P00268
Small Molecules
Ligands 5 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
OLC
Query on OLC

Download SDF File 
Download CCD File 
A
(2R)-2,3-dihydroxypropyl (9Z)-octadec-9-enoate
1-Oleoyl-R-glycerol
C21 H40 O4
RZRNAYUHWVFMIP-GDCKJWNLSA-N
 Ligand Interaction
ZN
Query on ZN

Download SDF File 
Download CCD File 
A
ZINC ION
Zn
PTFCDOFLOPIGGS-UHFFFAOYSA-N
 Ligand Interaction
GOL
Query on GOL

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Download CCD File 
A
GLYCEROL
GLYCERIN; PROPANE-1,2,3-TRIOL
C3 H8 O3
PEDCQBHIVMGVHV-UHFFFAOYSA-N
 Ligand Interaction
A8X
Query on A8X

Download SDF File 
Download CCD File 
A
3-[(3R)-3-[(4-fluorophenyl)sulfonylamino]-1,2,3,4-tetrahydrocarbazol-9-yl]propanoic acid
Ramatroban
C21 H21 F N2 O4 S
LDXDSHIEDAPSSA-OAHLLOKOSA-N
 Ligand Interaction
CLR
Query on CLR

Download SDF File 
Download CCD File 
A
CHOLESTEROL
C27 H46 O
HVYWMOMLDIMFJA-DPAQBDIFSA-N
 Ligand Interaction
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 2.5 Å
  • R-Value Free: 0.218 
  • R-Value Work: 0.198 
  • Space Group: C 2 2 21
Unit Cell:
Length (Å)Angle (°)
a = 81.160α = 90.00
b = 155.080β = 90.00
c = 128.130γ = 90.00
Software Package:
Software NamePurpose
XDSdata scaling
XDSdata reduction
BUSTERrefinement
PHASERphasing

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History & Funding Information

Deposition Data

  • Deposited Date: 2018-10-07 
  • Released Date: 2018-12-19 
  • Deposition Author(s): Fan, H., Zhao, Q., Wu, B.

Funding OrganizationLocationGrant Number
Chinese Academy of SciencesChinaQYZDB-SSW-SMC024

Revision History 

  • Version 1.0: 2018-12-19
    Type: Initial release
  • Version 1.1: 2018-12-26
    Type: Data collection, Database references