3WGU
Crystal structure of a Na+-bound Na+,K+-ATPase preceding the E1P state without oligomycin
- PDB DOI: https://doi.org/10.2210/pdb3WGU/pdb
- Classification: HYDROLASE/TRANSPORT PROTEIN
- Organism(s): Sus scrofa
- Mutation(s): No 
- Membrane Protein: Yes  OPMPDBTMMemProtMDmpstruc
- Deposited: 2013-08-09 Released: 2013-10-09 
Experimental Data Snapshot
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.299 
- R-Value Work: 0.265 
- R-Value Observed: 0.266 
wwPDB Validation   3D Report Full Report
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 |
Sodium/potassium-transporting ATPase subunit alpha-1 | A, D [auth C] | 1,016 | Sus scrofa | Mutation(s): 0  EC: 3.6.3.9 Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for P05024 (Sus scrofa) Explore P05024  Go to UniProtKB:  P05024 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P05024 | ||||
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 |
Sodium/potassium-transporting ATPase subunit beta-1 | B, E [auth D] | 303 | Sus scrofa | Mutation(s): 0  Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for P05027 (Sus scrofa) Explore P05027  Go to UniProtKB:  P05027 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | P05027 | ||||
Sequence AnnotationsExpand | |||||
|
Find similar proteins by:
(by identity cutoff) | 3D Structure
Entity ID: 3 | |||||
---|---|---|---|---|---|
Molecule | Chains | Sequence Length | Organism | Details | Image |
Na+/K+ ATPase gamma subunit transcript variant a | C [auth G], F [auth E] | 65 | Sus scrofa | Mutation(s): 0  Membrane Entity: Yes  | |
UniProt | |||||
Find proteins for Q58K79 (Sus scrofa) Explore Q58K79  Go to UniProtKB:  Q58K79 | |||||
Entity Groups   | |||||
Sequence Clusters | 30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity | ||||
UniProt Group | Q58K79 | ||||
Sequence AnnotationsExpand | |||||
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Small Molecules
Ligands 7 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
PC1 Query on PC1 | IA [auth C] JA [auth C] KA [auth C] LA [auth C] MA [auth D] | 1,2-DIACYL-SN-GLYCERO-3-PHOSPHOCHOLINE C44 H88 N O8 P NRJAVPSFFCBXDT-HUESYALOSA-N | |||
ADP Query on ADP | AA [auth C], J [auth A] | ADENOSINE-5'-DIPHOSPHATE C10 H15 N5 O10 P2 XTWYTFMLZFPYCI-KQYNXXCUSA-N | |||
CLR Query on CLR | FA [auth C] GA [auth C] HA [auth C] O [auth A] P [auth A] | CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N | |||
NAG Query on NAG | NA [auth D], W [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
ALF Query on ALF | H [auth A], Y [auth C] | TETRAFLUOROALUMINATE ION Al F4 UYOMQIYKOOHAMK-UHFFFAOYSA-J | |||
MG Query on MG | G [auth A], I [auth A], X [auth C], Z [auth C] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N | |||
NA Query on NA | BA [auth C] CA [auth C] DA [auth C] EA [auth C] K [auth A] | SODIUM ION Na FKNQFGJONOIPTF-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.80 Å
- R-Value Free: 0.299 
- R-Value Work: 0.265 
- R-Value Observed: 0.266 
- Space Group: P 21 21 21
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 106.383 | α = 90 |
b = 211.6 | β = 90 |
c = 257.124 | γ = 90 |
Software Name | Purpose |
---|---|
BSS | data collection |
PHASER | phasing |
PHENIX | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
Entry History 
Deposition Data
- Released Date: 2013-10-09  Deposition Author(s): Kanai, R., Ogawa, H., Vilsen, B., Cornelius, F., Toyoshima, C.
Revision History (Full details and data files)
- Version 1.0: 2013-10-09
Type: Initial release - Version 1.1: 2013-10-16
Changes: Database references - Version 1.2: 2020-07-29
Type: Remediation
Reason: Carbohydrate remediation
Changes: Data collection, Derived calculations, Structure summary