2DQS | pdb_00002dqs

Crystal structure of the calcium pump with amppcp in the absence of calcium

PDB DOI: https://doi.org/10.2210/pdb2DQS/pdb

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

Deposited: 2006-05-29 Released: 2007-06-05
Deposition Author(s): Toyoshima, C., Norimatsu, Y., Tsueda, J.

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free:
0.278 (Depositor)
R-Value Work:
0.234 (Depositor)
R-Value Observed:
0.234 (Depositor)

Starting Model: experimental
View more details

wwPDB Validation 3D Report Full Report

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

Literature

Crystal structure of the calcium pump with a bound ATP analogue in the absence of calcium

Toyoshima, C., Norimatsu, Y., Tsueda, J.

To be published.

Macromolecule Content

Total Structure Weight: 112.32 kDa
Atom Count: 8,024
Modeled Residue Count: 995
Deposited Residue Count: 995
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	995	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 5 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
PTY Query on PTY Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain G [auth A] MOL2 format, chain H [auth A] MOL2 format, chain G [auth A] mmCIF format, chain H [auth A] mmCIF format, chain G [auth A]	G [auth A], H [auth A]	PHOSPHATIDYLETHANOLAMINE C₄₀ H₈₀ N O₈ P NJGIRBISCGPRPF-KXQOOQHDSA-N		Interactions Focus chain G [auth A] Focus chain H [auth A]
TG1 Query on TG1 Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A] mmCIF format, chain F [auth A]	F [auth A]	OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA, 6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OX Y]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER C₃₄ H₅₀ O₁₂ IXFPJGBNCFXKPI-FSIHEZPISA-N		Interactions Focus chain F [auth A]
ACP Query on ACP Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A] mmCIF format, chain E [auth A]	E [auth A]	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER C₁₁ H₁₈ N₅ O₁₂ P₃ UFZTZBNSLXELAL-IOSLPCCCSA-N		Interactions Focus chain E [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain D [auth A] SDF format, chain B [auth A] MOL2 format, chain D [auth A] MOL2 format, chain B [auth A] mmCIF format, chain D [auth A] mmCIF format, chain B [auth A]	B [auth A], D [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain B [auth A] Focus chain D [auth A]
NA Query on NA 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]	SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N		Interactions Focus chain C [auth A]

Binding Affinity Annotations
ID	Source	Binding Affinity
TG1	BindingDB: 2DQS	Ki: 0.1 (nM) from 1 assay(s)
		Kd: 0.2 (nM) from 1 assay(s)
		IC50: min: 0.2, max: 3.9 (nM) from 2 assay(s)

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.50 Å
R-Value Free: 0.278 (Depositor)
R-Value Work: 0.234 (Depositor)
R-Value Observed: 0.234 (Depositor)

Space Group: P 4₁ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 71.421	α = 90
b = 71.421	β = 90
c = 589.756	γ = 90

Software Package:

Software Name	Purpose
CNS	refinement
DENZO	data reduction
SCALEPACK	data scaling
CNS	phasing

Structure Validation

View Full Validation Report

Entry History

Deposition Data

Released Date: 2007-06-05

Deposition Author(s):

Toyoshima, C.

Norimatsu, Y.

Tsueda, J.

Revision History (Full details and data files)

Version 1.0: 2007-06-05
Type: Initial release
Version 1.1: 2008-04-25
Changes: Version format compliance
Version 1.2: 2011-07-13
Changes: Non-polymer description, Version format compliance
Version 1.3: 2023-10-25
Changes: Data collection, Database references, Derived calculations, Refinement description, Structure summary
Version 1.4: 2024-10-30
Changes: Structure summary