3A3Y
Crystal structure of the sodium-potassium pump with bound potassium and ouabain
- PDB DOI: https://doi.org/10.2210/pdb3A3Y/pdb
- Classification: HYDROLASE/TRANSPORT PROTEIN
- Organism(s): Squalus acanthias
- Mutation(s): No 
- Membrane Protein: Yes  PDBTMMemProtMDmpstruc
- Deposited: 2009-06-23 Released: 2009-09-08 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.293 
- R-Value Work: 0.247 
- R-Value Observed: 0.249 
This is version 1.2 of the entry. See complete history. 
Macromolecules
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 1 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Na, K-ATPase alpha subunit | 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 AnnotationsExpand | |||||
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Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 2 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
NA+,K+-ATPASE BETA SUBUNIT | 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 AnnotationsExpand | |||||
|
Find similar proteins by:
(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 AnnotationsExpand | |||||
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Small Molecules
Ligands 6 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
OBN Query on OBN | I [auth A] | OUABAIN C29 H44 O12 LPMXVESGRSUGHW-HBYQJFLCSA-N | |||
CLR Query on CLR | J [auth B] | CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N | |||
NAG Query on NAG | K [auth B], L [auth B], M [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
MF4 Query on MF4 | D [auth A] | TETRAFLUOROMAGNESATE(2-) F4 Mg XVYWAXYEHHUKQW-UHFFFAOYSA-J | |||
K Query on K | F [auth A], G [auth A], H [auth A] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N | |||
MG Query on MG | E [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.293 
- R-Value Work: 0.247 
- R-Value Observed: 0.249 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 222.884 | α = 90 |
b = 50.72 | β = 104.63 |
c = 163.342 | γ = 90 |
Software Name | Purpose |
---|---|
REFMAC | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |
Entry History 
Deposition Data
- Released Date: 2009-09-08  Deposition Author(s): Ogawa, H., Shinoda, T., Cornelius, F., Toyoshima, C.
Revision History (Full details and data files)
- Version 1.0: 2009-09-08
Type: Initial release - Version 1.1: 2011-07-13
Changes: Advisory, Version format compliance - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary