4J2T

Inhibitor-bound Ca2+ ATPase


Experimental Data Snapshot

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.260 

wwPDB Validation 3D Report Full Report


This is version 1.1 of the entry. See complete history

Literature

Water-mediated interactions influence the binding of thapsigargin to sarco/endoplasmic reticulum calcium adenosinetriphosphatase.

Paulsen, E.S.Villadsen, J.Tenori, E.Liu, H.Bonde, D.F.Lie, M.A.Bublitz, M.Olesen, C.Autzen, H.E.Dach, I.Sehgal, P.Nissen, P.Moller, J.V.Schiott, B.Christensen, S.B.

(2013) J.Med.Chem. 56: 3609-3619

  • DOI: 10.1021/jm4001083

  • PubMed Abstract: 
  • A crystal structure suggests four water molecules are present in the binding cavity of thapsigargin in sarco/endoplasmic reticulum calcium ATPase (SERCA). Computational chemistry indicates that three of these water molecules mediate an extensive hydr ...

    A crystal structure suggests four water molecules are present in the binding cavity of thapsigargin in sarco/endoplasmic reticulum calcium ATPase (SERCA). Computational chemistry indicates that three of these water molecules mediate an extensive hydrogen-bonding network between thapsigargin and the backbone of SERCA. The orientation of the thapsigargin molecule in SERCA is crucially dependent on these interactions. The hypothesis has been verified by measuring the affinity of newly synthesized model compounds, which are prevented from participating in such water-mediated interactions as hydrogen-bond donors.


    Organizational Affiliation

    Department of Drug Design and Pharmacology, Faculty of Health and Medical Sciences, University of Copenhagen, Universitetsparken 2, DK-2100 Copenhagen Ø, Denmark.




Macromolecules

Find similar proteins by: Sequence  |  Structure

Entity ID: 1
MoleculeChainsSequence LengthOrganismDetails
SERCA1a
A
994Oryctolagus cuniculusMutation(s): 0 
Gene Names: ATP2A1
EC: 7.2.2.10
Find proteins for P04191 (Oryctolagus cuniculus)
Go to Gene View: ATP2A1
Go to UniProtKB:  P04191
Small Molecules
Ligands 3 Unique
IDChainsName / Formula / InChI Key2D Diagram3D Interactions
K
Query on K

Download SDF File 
Download CCD File 
A
POTASSIUM ION
K
NPYPAHLBTDXSSS-UHFFFAOYSA-N
 Ligand Interaction
PTY
Query on PTY

Download SDF File 
Download CCD File 
A
PHOSPHATIDYLETHANOLAMINE
C40 H80 N O8 P
NJGIRBISCGPRPF-KXQOOQHDSA-N
 Ligand Interaction
1HT
Query on 1HT

Download SDF File 
Download CCD File 
A
(3S,3aR,4S,6S,6aR,7S,8S,9bS)-6-(acetyloxy)-3a,4-bis(butanoyloxy)-3-hydroxy-3,6,9-trimethyl-8-{[(2E)-2-methylbut-2-enoyl]oxy}-2-oxo-2,3,3a,4,5,6,6a,7,8,9b-decahydroazuleno[4,5-b]furan-7-yl octanoate
C38 H56 O13
ARWTVHVQANENHV-XDRCOMTCSA-N
 Ligand Interaction
External Ligand Annotations 
IDBinding Affinity (Sequence Identity %)
1HTKd: 11 nM PDBBIND
Experimental Data & Validation

Experimental Data

  • Method: X-RAY DIFFRACTION
  • Resolution: 3.2 Å
  • R-Value Free: 0.286 
  • R-Value Work: 0.260 
  • Space Group: P 41 21 2
Unit Cell:
Length (Å)Angle (°)
a = 70.900α = 90.00
b = 70.900β = 90.00
c = 587.600γ = 90.00
Software Package:
Software NamePurpose
XSCALEdata scaling
PHENIXrefinement
PHASERphasing
MAXLABdata collection
XDSdata reduction

Structure Validation

View Full Validation Report or Ramachandran Plots



Entry History 

Deposition Data

Revision History 

  • Version 1.0: 2013-06-19
    Type: Initial release
  • Version 1.1: 2018-01-24
    Type: Data collection, Structure summary