5AW1

Kinetics by X-ray crystallography: Tl+-substitution of bound K+ in the E2.MgF42-.2K+ crystal after 85 min

PDB DOI: https://doi.org/10.2210/pdb5AW1/pdb

Classification: HYDROLASE/TRANSPORT PROTEIN
Organism(s): Squalus acanthias
Mutation(s): No
Membrane Protein: Yes PDBTMMemProtMDmpstruc

Deposited: 2015-07-01 Released: 2015-09-02
Deposition Author(s): Ogawa, H., Cornelius, F., Hirata, A., Toyoshima, C.
Funding Organization(s): Ministry of Education, Culture, Sports, Science and Technology of Japan, The Danish Medical Research Foundation, The Danish Agency for Science Technology and Innovation, The Novo Nordisk Foundation

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.305
R-Value Work: 0.297
R-Value Observed: 0.297

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 of the entry. See complete history.

Macromolecule Content

Total Structure Weight: 158.56 kDa
Atom Count: 10,236
Modelled Residue Count: 1,299
Deposited Residue Count: 1,407
Unique protein chains: 3

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Na, K-ATPase alpha subunit	A	1,028	Squalus acanthias	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q4H132 (Squalus acanthias) Explore Q4H132 Go to UniProtKB: Q4H132
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q4H132
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 2
Molecule	Chains	Sequence Length	Organism	Details	Image
Na+,K+-ATPase beta subunit	B	305	Squalus acanthias	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for C4IX13 (Squalus acanthias) Explore C4IX13 Go to UniProtKB: C4IX13
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	C4IX13
Sequence Annotations Expand
Reference Sequence

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(by identity cutoff) | 3D Structure

Entity ID: 3
Molecule	Chains	Sequence Length	Organism	Details	Image
Phospholemman-like protein	C [auth G]	74	Squalus acanthias	Mutation(s): 0 Membrane Entity: Yes
UniProt
Find proteins for Q70Q12 (Squalus acanthias) Explore Q70Q12 Go to UniProtKB: Q70Q12
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q70Q12
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 4
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	D [auth C]	2		N-Glycosylation	Interactions Focus chain D [auth C] Interactions & Density Focus chain D [auth C]
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 6 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
CLR Query on CLR Download Ideal Coordinates CCD File SDF format, chain L [auth B] MOL2 format, chain L [auth B]	L [auth B]	CHOLESTEROL C₂₇ H₄₆ O HVYWMOMLDIMFJA-DPAQBDIFSA-N		Interactions Focus chain L [auth B] Interactions & Density Focus chain L [auth B]
NAG Query on NAG Download Ideal Coordinates CCD File SDF format, chain M [auth B] MOL2 format, chain M [auth B]	M [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain M [auth B] Interactions & Density Focus chain M [auth B]
TL Query on TL Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain K [auth A] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain K [auth A]	H [auth A], I [auth A], K [auth A]	THALLIUM (I) ION Tl ZLUSCZLCHQSJRU-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain K [auth A]
MF4 Query on MF4 Download Ideal Coordinates CCD File SDF format, chain E [auth A] MOL2 format, chain E [auth A]	E [auth A]	TETRAFLUOROMAGNESATE(2-) F₄ Mg XVYWAXYEHHUKQW-UHFFFAOYSA-J		Interactions Focus chain E [auth A] Interactions & Density Focus chain E [auth A]
K Query on K Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain J [auth A] MOL2 format, chain G [auth A] MOL2 format, chain J [auth A]	G [auth A], J [auth A]	POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N		Interactions Focus chain G [auth A] Focus chain J [auth A] Interactions & Density Focus chain G [auth A] Focus chain J [auth A]
MG Query on MG Download Ideal Coordinates CCD File SDF format, chain F [auth A] MOL2 format, chain F [auth A]	F [auth A]	MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N		Interactions Focus chain F [auth A] Interactions & Density Focus chain F [auth A]

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 3.35 Å
R-Value Free: 0.305
R-Value Work: 0.297
R-Value Observed: 0.297
Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 222.035	α = 90
b = 50.855	β = 104.02
c = 163.971	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2015-09-02

Deposition Author(s):

Funding Organization	Location	Grant Number
Ministry of Education, Culture, Sports, Science and Technology of Japan	Japan	--
The Danish Medical Research Foundation	Denmark	--
The Danish Agency for Science Technology and Innovation	Denmark	--
The Novo Nordisk Foundation	Denmark	--

Revision History (Full details and data files)

Version 1.0: 2015-09-02
Type: Initial release
Version 1.1: 2020-02-26
Changes: Data collection, Derived calculations, Source and taxonomy
Version 2.0: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Atomic model, Data collection, Derived calculations, Structure summary
Version 2.1: 2023-11-08
Changes: Data collection, Database references, Refinement description, Structure summary