8OWA | pdb_00008owa

SR Ca(2+)-ATPase in the E2 state complexed with the photoswitch-thapsigargin derivative AzTG-4

PDB DOI: https://doi.org/10.2210/pdb8OWA/pdb

Classification: HYDROLASE
Organism(s): Oryctolagus cuniculus
Mutation(s): No
Membrane Protein: Yes PDBTM MemProtMD

Deposited: 2023-04-27 Released: 2023-06-21
Deposition Author(s): Hjorth-Jensen, S.J., Konrad, D.B., Quistgaard, E.M.H., Hansen, L.C., Novak, A., Chu, H., Jurasek, M., Zimmermann, T., Andersen, J.L., Baran, P.S., Nissen, P., Trauner, D.
Funding Organization(s): German Research Foundation (DFG), H2020 Marie Curie Actions of the European Commission, Lundbeckfonden

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free:
0.279 (Depositor), 0.278 (DCC)
R-Value Work:
0.243 (Depositor), 0.244 (DCC)
R-Value Observed:
0.244 (Depositor)

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.0 of the entry. See complete history.

Literature

Photoswitchable inhibitors of the sarco(endo)plasmic calcium pump

Hjorth-Jensen, S.J., Konrad, D.B., Quistgaard, E.M.H., Hansen, L.C., Novak, A., Chu, H., Jurasek, M., Zimmermann, T., Andersen, J.L., Baran, P.S., Nissen, P., Trauner, D.

To be published.

Macromolecule Content

Total Structure Weight: 110.2 kDa
Atom Count: 7,640
Modeled Residue Count: 981
Deposited Residue Count: 991
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Sarcoplasmic/endoplasmic reticulum calcium ATPase 1	A	991	Oryctolagus cuniculus	Mutation(s): 0 EC: 7.2.2.10 Membrane Entity: Yes
UniProt
Find proteins for P04191 (Oryctolagus cuniculus) Explore P04191 Go to UniProtKB: P04191
Entity Groups
Sequence Clusters	30% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	P04191
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
VUK (Subject of Investigation/LOI) Query on VUK Download:Ideal Coordinates CCD File SDF format, chain C [auth A] MOL2 format, chain C [auth A] mmCIF format, chain C [auth A]	C [auth A]	[(3S,3aR,4S,6S,6aR,7S,8S,9bS)-6-acetyloxy-3,6,9-trimethyl-8-[(Z)-2-methylbut-2-enoyl]oxy-3,3a-bis(oxidanyl)-2-oxidanylidene-4-[4-[4-[(E)-phenyldiazenyl]phenyl]butanoyloxy]-4,5,6a,7,8,9b-hexahydroazuleno[4,5-b]furan-7-yl] octanoate C₄₆ H₅₈ N₂ O₁₂ NGXFGRHJQLJRQJ-RCNCXLEOSA-N		Interactions Focus chain C [auth A] Interactions & Density Focus chain C [auth A]
ACE Query on ACE Download:Ideal Coordinates CCD File SDF format, chain B [auth A] MOL2 format, chain B [auth A] mmCIF format, chain B [auth A]	B [auth A]	ACETYL GROUP C₂ H₄ O IKHGUXGNUITLKF-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Interactions & Density Focus chain B [auth A]
NA Query on NA Download:Ideal Coordinates CCD File SDF format, chain D [auth A] MOL2 format, chain D [auth A] mmCIF format, chain D [auth A]	D [auth A]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Interactions & Density Focus chain D [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.85 Å
R-Value Free: 0.279 (Depositor), 0.278 (DCC)
R-Value Work: 0.243 (Depositor), 0.244 (DCC)
R-Value Observed: 0.244 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.31	α = 90
b = 71.31	β = 90
c = 586.81	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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Entry History

& Funding Information

Deposition Data

Released Date: 2023-06-21

Deposition Author(s):

Funding Organization	Location	Grant Number
German Research Foundation (DFG)	Germany	239283807
H2020 Marie Curie Actions of the European Commission	European Union	722687
Lundbeckfonden	Denmark	R310-2018-3713