PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3A3Y
Asym. Unit
Info
Asym.Unit (217 KB)
Biol.Unit 1 (209 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF THE SODIUM-POTASSIUM PUMP WITH BOUND POTASSIUM AND OUABAIN
Authors
:
H. Ogawa, T. Shinoda, F. Cornelius, C. Toyoshima
Date
:
23 Jun 09 (Deposition) - 08 Sep 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,G
Biol. Unit 1: A,B,G (1x)
Keywords
:
Membrane Protein, Ion Pump, Atpase, K+ Binding, Ouabain Binding, Haloacid Dehydrogenease Superfamily, Phosphate Analogue, Atp- Binding, Hydrolase, Ion Transport, Nucleotide-Binding, Phosphoprotein, Hydrolase-Transport Protein Complex, Membrane, Transmembrane, Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Ogawa, T. Shinoda, F. Cornelius, C. Toyoshima
Crystal Structure Of The Sodium-Potassium Pump (Na+, K+-Atpase) With Bound Potassium And Ouabain.
Proc. Natl. Acad. Sci. Usa V. 106 13742 2009
[
close entry info
]
Hetero Components
(6, 10)
Info
All Hetero Components
1a: CHOLESTEROL (CLRa)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
3a: TETRAFLUOROMAGNESATE(2-) (MF4a)
4a: MAGNESIUM ION (MGa)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6a: OUABAIN (OBNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CLR
1
Ligand/Ion
CHOLESTEROL
2
K
3
Ligand/Ion
POTASSIUM ION
3
MF4
1
Ligand/Ion
TETRAFLUOROMAGNESATE(2-)
4
MG
1
Ligand/Ion
MAGNESIUM ION
5
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
OBN
1
Ligand/Ion
OUABAIN
[
close Hetero Component info
]
Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:219 , GLY A:220 , GLU A:221 , ASP A:376 , LYS A:377 , THR A:378 , THR A:617 , GLY A:618 , ASP A:619 , LYS A:698 , ASN A:720 , MG A:2002 , HOH A:5024 , HOH A:5026
BINDING SITE FOR RESIDUE MF4 A 2001
02
AC2
SOFTWARE
ASP A:376 , THR A:378 , ASP A:717 , MF4 A:2001 , HOH A:5024 , HOH A:5026
BINDING SITE FOR RESIDUE MG A 2002
03
AC3
SOFTWARE
THR A:779 , SER A:782 , ASN A:783 , GLU A:786 , ASP A:811 , HOH A:5006
BINDING SITE FOR RESIDUE K A 2003
04
AC4
SOFTWARE
VAL A:329 , ALA A:330 , VAL A:332 , GLU A:334 , ASN A:783 , GLU A:786 , ASP A:811
BINDING SITE FOR RESIDUE K A 2004
05
AC5
SOFTWARE
ALA A:728 , ASP A:747
BINDING SITE FOR RESIDUE K A 2005
06
AC6
SOFTWARE
PHE A:323 , GLY A:326 , ILE A:327 , ILE A:328 , VAL A:329 , ALA A:330 , PHE A:790 , THR A:804 , ARG A:887
BINDING SITE FOR RESIDUE OBN A 6000
07
AC7
SOFTWARE
SER A:851 , TYR B:40 , TYR B:44
BINDING SITE FOR RESIDUE CLR B 3001
08
AC8
SOFTWARE
ASP B:111 , ASN B:114 , ARG B:154 , NAG B:4002
BINDING SITE FOR RESIDUE NAG B 4001
09
AC9
SOFTWARE
NAG B:4001
BINDING SITE FOR RESIDUE NAG B 4002
10
BC1
SOFTWARE
ASN B:159
BINDING SITE FOR RESIDUE NAG B 4021
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(6, 6)
Info
all CATH domains
1a: CATH_3a3yA04 (A:384-594)
2a: CATH_3a3yA03 (A:371-383,A:595-755)
3a: CATH_3a3yA02 (A:94-147,A:277-370,A:756-1023)
4a: CATH_3a3yB01 (B:28-62)
5a: CATH_3a3yA01 (A:32-77,A:157-276)
6a: CATH_3a3yB02 (B:63-305)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Calcium-transporting ATPase, cytoplasmic domain N
(43)
Homologous Superfamily
:
Calcium-transporting ATPase, cytoplasmic domain N
(43)
Spiny dogfish (Squalus acanthias)
(2)
1a
3a3yA04
A:384-594
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.1000, no name defined]
(211)
Spiny dogfish (Squalus acanthias)
(2)
2a
3a3yA03
A:371-383,A:595-755
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Calcium-transporting ATPase, transmembrane domain
(36)
Homologous Superfamily
:
Calcium-transporting ATPase, transmembrane domain
(36)
Spiny dogfish (Squalus acanthias)
(2)
3a
3a3yA02
A:94-147,A:277-370,A:756-1023
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.170, no name defined]
(60)
Spiny dogfish (Squalus acanthias)
(2)
4a
3a3yB01
B:28-62
Class
:
Mainly Beta
(13760)
Architecture
:
Distorted Sandwich
(506)
Topology
:
Calcium-transporting ATPase, cytoplasmic transduction domain A
(35)
Homologous Superfamily
:
Calcium-transporting ATPase, cytoplasmic transduction domain A
(35)
Spiny dogfish (Squalus acanthias)
(2)
5a
3a3yA01
A:32-77,A:157-276
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Na, k-atpase alpha subunit.
(3)
Spiny dogfish (Squalus acanthias)
(2)
6a
3a3yB02
B:63-305
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Chain G
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (217 KB)
Header - Asym.Unit
Biol.Unit 1 (209 KB)
Header - Biol.Unit 1
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
3A3Y
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
