4BEW | pdb_00004bew

SERCA bound to phosphate analogue

• PDB DOI: https://doi.org/10.2210/pdb4BEW/pdb

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


• Deposited: 2013-03-12 Released: 2014-02-19 
• Deposition Author(s): Drachmann, N.D., Mattle, D., Laursen, M., Bublitz, M., Olesen, C., Moeller, J.V., Nissen, P., Morth, J.P.

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free: 
  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work: 
  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 
  0.170 (Depositor) 

Starting Model: experimental

Literature

Serca Bound to Phosphate Analogue

Mattle, D., Drachmann, N.D., Liu, X.Y., Gourdon, P., Pedersen, B.P., Morth, P., Wang, J., Nissen, P.

To be published.

Biological Assembly 1  

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

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

Biological Assembly 2  

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

Biological assembly 2 assigned by authors and generated by PISA (software)

Macromolecule Content 

• Total Structure Weight: 221.69 kDa 
• Atom Count: 15,950 
• Modeled Residue Count: 1,988 
• Deposited Residue Count: 1,988 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
SARCOPLASMIC/ENDOPLASMIC RETICULUM CALCIUM ATPASE 1	A, B	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 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
ACP	G [auth A], P [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C11 H18 N5 O12 P3 UFZTZBNSLXELAL-IOSLPCCCSA-N
CZA	E [auth A], N [auth B]	(6AR,11AS,11BR)-10-ACETYL-9-HYDROXY-7,7-DIMETHYL-2,6,6A,7,11A,11B-HEXAHYDRO-11H-PYRROLO[1',2':2,3]ISOINDOLO[4,5,6-CD]INDOL-11-ONE C20 H20 N2 O3 RLOAZVAJNNPPDI-DQYPLSBCSA-N
MGF	I [auth A], Q [auth B]	TRIFLUOROMAGNESATE F3 Mg GJOMWUHGUQLOAC-UHFFFAOYSA-K
ACT	J [auth A], K [auth A], R [auth B], S [auth B]	ACETATE ION C2 H3 O2 QTBSBXVTEAMEQO-UHFFFAOYSA-M
MN	F [auth A], H [auth A], O [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N
K	D [auth A], M [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N
MG	C [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.50 Å
• R-Value Free:  0.207 (Depositor), 0.210 (DCC) 
• R-Value Work:  0.169 (Depositor), 0.173 (DCC) 
• R-Value Observed: 0.170 (Depositor) 

Space Group: P 2₁ 2₁ 2₁

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 101.43	α = 90
b = 108.87	β = 90
c = 274.31	γ = 90

Software Package:

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

Structure Validation

Entry History 

Deposition Data

• Released Date: 2014-02-19 
Deposition Author(s): Drachmann, N.D., Mattle, D., Laursen, M., Bublitz, M., Olesen, C., Moeller, J.V., Nissen, P., Morth, J.P.

Revision History  

• Version 1.0: 2014-02-19
  Type: Initial release
  
• Version 1.1: 2019-01-30
  Changes: Data collection, Experimental preparation, Other
• Version 1.2: 2019-02-06
  Changes: Data collection, Experimental preparation
• Version 1.3: 2023-12-20
  Changes: Data collection, Database references, Derived calculations, Other, Refinement description
• Version 1.4: 2024-11-20
  Changes: Structure summary