4J2T | pdb_00004j2t

Inhibitor-bound Ca2+ ATPase

• PDB DOI: https://doi.org/10.2210/pdb4J2T/pdb

• Classification: HYDROLASE/HYDROLASE INHIBITOR
• Organism(s): Oryctolagus cuniculus
• Mutation(s): No 
• Membrane Protein: Yes  PDBTMMemProtMD


• Deposited: 2013-02-05 Released: 2013-06-19 
• Deposition Author(s): Paulsen, E.S., Villadsen, J., Tenori, E., Liu, H., Lie, M.A., Bonde, D.F., Bublitz, M., Olesen, C., Autzen, H.E., Dach, I., Sehgal, P., Moller, J.V., Schiott, B., Nissen, P., Christensen, S.B.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free: 
  0.286 (Depositor), 0.287 (DCC) 
• R-Value Work: 
  0.260 (Depositor), 0.263 (DCC) 
• R-Value Observed: 
  0.262 (Depositor) 

Starting Model: experimental

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

• PubMed: 23574308 
• DOI: https://doi.org/10.1021/jm4001083
• Primary Citation Related Structures: 
  4J2T


• 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 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.

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

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 111.1 kDa 
• Atom Count: 7,748 
• Modeled Residue Count: 994 
• Deposited Residue Count: 994 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SERCA1a	A	994	Oryctolagus cuniculus	Mutation(s): 0  EC: 3.6.3.8 (PDB Primary Data), 7.2.2.10 (UniProt) Membrane Entity: Yes
UniProt
Find proteins for P04191 (Oryctolagus cuniculus) Explore P04191  Go to UniProtKB:  P04191

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
PTY	C [auth A]	PHOSPHATIDYLETHANOLAMINE C40 H80 N O8 P NJGIRBISCGPRPF-KXQOOQHDSA-N
1HT	B [auth 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
K	D [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 3.20 Å
• R-Value Free:  0.286 (Depositor), 0.287 (DCC) 
• R-Value Work:  0.260 (Depositor), 0.263 (DCC) 
• R-Value Observed: 0.262 (Depositor) 

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 70.9	α = 90
b = 70.9	β = 90
c = 587.6	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2013-06-19 
Deposition Author(s): Paulsen, E.S., Villadsen, J., Tenori, E., Liu, H., Lie, M.A., Bonde, D.F., Bublitz, M., Olesen, C., Autzen, H.E., Dach, I., Sehgal, P., Moller, J.V., Schiott, B., Nissen, P., Christensen, S.B.

Revision History  

• Version 1.0: 2013-06-19
  Type: Initial release
  
• Version 1.1: 2018-01-24
  Changes: Data collection, Structure summary
• Version 1.2: 2023-09-20
  Changes: Data collection, Database references, Derived calculations, Refinement description
• Version 1.3: 2024-10-16
  Changes: Structure summary