5AVV
Kinetics by X-ray crystallography: Tl+-substitution of bound K+ in the E2.MgF42-.2K+ crystal after 8.5 min
- PDB DOI: https://doi.org/10.2210/pdb5AVV/pdb
- Classification: HYDROLASE/TRANSPORT PROTEIN
- Organism(s): Squalus acanthias
- Mutation(s): No 
- Membrane Protein: Yes  PDBTMMemProtMDmpstruc
- Deposited: 2015-07-01 Released: 2015-09-02 
- 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: 2.90 Å
- R-Value Free: 0.293 
- R-Value Work: 0.279 
- R-Value Observed: 0.279 
This is version 2.1 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 | |||||
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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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Oligosaccharides
Small Molecules
Ligands 6 Unique | |||||
---|---|---|---|---|---|
ID | Chains | Name / Formula / InChI Key | 2D Diagram | 3D Interactions | |
CLR Query on CLR | K [auth B] | CHOLESTEROL C27 H46 O HVYWMOMLDIMFJA-DPAQBDIFSA-N | |||
NAG Query on NAG | L [auth B] | 2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N | |||
TL Query on TL | G [auth A], H [auth A], J [auth A] | THALLIUM (I) ION Tl ZLUSCZLCHQSJRU-UHFFFAOYSA-N | |||
MF4 Query on MF4 | E [auth A] | TETRAFLUOROMAGNESATE(2-) F4 Mg XVYWAXYEHHUKQW-UHFFFAOYSA-J | |||
K Query on K | I [auth A] | POTASSIUM ION K NPYPAHLBTDXSSS-UHFFFAOYSA-N | |||
MG Query on MG | F [auth A] | MAGNESIUM ION Mg JLVVSXFLKOJNIY-UHFFFAOYSA-N |
Experimental Data & Validation
Experimental Data
- Method: X-RAY DIFFRACTION
- Resolution: 2.90 Å
- R-Value Free: 0.293 
- R-Value Work: 0.279 
- R-Value Observed: 0.279 
- Space Group: C 1 2 1
Unit Cell:
Length ( Å ) | Angle ( ˚ ) |
---|---|
a = 220.991 | α = 90 |
b = 50.841 | β = 104.02 |
c = 163.358 | γ = 90 |
Software Name | Purpose |
---|---|
CNS | refinement |
DENZO | data reduction |
SCALEPACK | data scaling |
CNS | phasing |
Entry History & Funding Information
Deposition Data
- Released Date: 2015-09-02  Deposition Author(s): Ogawa, H., Cornelius, F., Hirata, A., Toyoshima, C.
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