4BEW

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.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.207
R-Value Work: 0.169
R-Value Observed: 0.170

Starting Model: experimental
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 1.4 of the entry. See complete history.

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.

Macromolecule Content

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

Macromolecules

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(by identity cutoff) | 3D Structure

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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	P04191
Sequence Annotations Expand
Reference Sequence

Small Molecules

Ligands 7 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain P [auth B] MOL2 format, chain G [auth A] MOL2 format, chain P [auth B] mmCIF format, chain G [auth A] mmCIF format, chain P [auth B]	G [auth A], P [auth B]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain G [auth A] Focus chain P [auth B] Interactions & Density Focus chain G [auth A] Focus chain P [auth B]
CZA Query on CZA Download Ideal Coordinates CCD File SDF format, chain E [auth A] SDF format, chain N [auth B] MOL2 format, chain E [auth A] MOL2 format, chain N [auth B] mmCIF format, chain E [auth A] mmCIF format, chain N [auth B]	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		Interactions Focus chain E [auth A] Focus chain N [auth B] Interactions & Density Focus chain E [auth A] Focus chain N [auth B]
MGF Query on MGF Download Ideal Coordinates CCD File SDF format, chain I [auth A] SDF format, chain Q [auth B] MOL2 format, chain I [auth A] MOL2 format, chain Q [auth B] mmCIF format, chain I [auth A] mmCIF format, chain Q [auth B]	I [auth A], Q [auth B]	TRIFLUOROMAGNESATE F₃ Mg GJOMWUHGUQLOAC-UHFFFAOYSA-K		Interactions Focus chain I [auth A] Focus chain Q [auth B] Interactions & Density Focus chain I [auth A] Focus chain Q [auth B]
ACT Query on ACT Download Ideal Coordinates CCD File SDF format, chain J [auth A] SDF format, chain K [auth A] SDF format, chain R [auth B] SDF format, chain S [auth B] MOL2 format, chain J [auth A] MOL2 format, chain K [auth A] MOL2 format, chain R [auth B] MOL2 format, chain S [auth B] mmCIF format, chain J [auth A] mmCIF format, chain K [auth A] mmCIF format, chain R [auth B] mmCIF format, chain S [auth B]	J [auth A], K [auth A], R [auth B], S [auth B]	ACETATE ION C₂ H₃ O₂ QTBSBXVTEAMEQO-UHFFFAOYSA-M		Interactions Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B] Interactions & Density Focus chain J [auth A] Focus chain K [auth A] Focus chain R [auth B] Focus chain S [auth B]
MN Query on MN Download Ideal Coordinates CCD File SDF format, chain F [auth A] SDF format, chain H [auth A] SDF format, chain O [auth B] MOL2 format, chain F [auth A] MOL2 format, chain H [auth A] MOL2 format, chain O [auth B] mmCIF format, chain F [auth A] mmCIF format, chain H [auth A] mmCIF format, chain O [auth B]	F [auth A], H [auth A], O [auth B]	MANGANESE (II) ION Mn WAEMQWOKJMHJLA-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Focus chain H [auth A] Focus chain O [auth B] Interactions & Density Focus chain F [auth A] Focus chain H [auth A] Focus chain O [auth B]
K Query on K Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain M [auth B] MOL2 format, chain D [auth A] MOL2 format, chain M [auth B] mmCIF format, chain D [auth A] mmCIF format, chain M [auth B]	D [auth A], M [auth B]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain D [auth A] Focus chain M [auth B] Interactions & Density Focus chain D [auth A] Focus chain M [auth B]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain C [auth A] SDF format, chain L [auth B] MOL2 format, chain C [auth A] MOL2 format, chain L [auth B] mmCIF format, chain C [auth A] mmCIF format, chain L [auth B]	C [auth A], L [auth B]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain C [auth A] Focus chain L [auth B] Interactions & Density Focus chain C [auth A] Focus chain L [auth B]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.207
R-Value Work: 0.169
R-Value Observed: 0.170
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

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Ligand Structure Quality Assessment

Entry History

Deposition Data

Released Date: 2014-02-19

Deposition Author(s):

Revision History (Full details and data files)

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