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.
3AR5
Asym. Unit
Info
Asym.Unit (335 KB)
Biol.Unit 1 (328 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CALCIUM PUMP CRYSTAL STRUCTURE WITH BOUND TNP-AMP AND TG
Authors
:
C. Toyoshima, S. Yonekura, J. Tsueda, S. Iwasawa
Date
:
24 Nov 10 (Deposition) - 02 Feb 11 (Release) - 31 Jul 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
P-Type Atpase, Hydrolase, Calcium Transport, Calcium Binding, Atp Binding, Endoplasmic Reticulum, Sarcoplasmic Reticulum, Hydrolase- Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Toyoshima, S. Yonekura, J. Tsueda, S. Iwasawa
Trinitrophenyl Derivatives Bind Differently From Parent Adenine Nucleotides To Ca2+-Atpase In The Absence Of Ca2+
Proc. Natl. Acad. Sci. Usa V. 108 1833 2011
[
close entry info
]
Hetero Components
(5, 7)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
2a: SODIUM ION (NAa)
3a: PHOSPHATIDYLETHANOLAMINE (PTYa)
3b: PHOSPHATIDYLETHANOLAMINE (PTYb)
3c: PHOSPHATIDYLETHANOLAMINE (PTYc)
4a: OCTANOIC ACID [3S-[3ALPHA, 3ABETA,... (TG1a)
5a: 2',3'-O-[(1R)-2,4,6-TRINITROCYCLOH... (TM1a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
1
Mod. Amino Acid
ACETYL GROUP
2
NA
1
Ligand/Ion
SODIUM ION
3
PTY
3
Ligand/Ion
PHOSPHATIDYLETHANOLAMINE
4
TG1
1
Ligand/Ion
OCTANOIC ACID [3S-[3ALPHA, 3ABETA, 4ALPHA, 6BETA,6ABETA, 7BETA, 8ALPHA(Z), 9BALPHA]]-6-(ACETYLOXY)-2,3,-3A,4,5,6,6A,7,8,9B-DECAHYDRO-3,3A-DIHYDROXY-3,6,9-TRIMETHYL-8-[(2-METHYL-1-OXO-2-BUTENYL)OXY]-2-OXO-4-(1-OXOBUTOXY)-AZULENO[4,5-B]FURAN-7-YL ESTER
5
TM1
1
Ligand/Ion
2',3'-O-[(1R)-2,4,6-TRINITROCYCLOHEXA-2,5-DIENE-1,1-DIYL]ADENOSINE 5'-(DIHYDROGEN PHOSPHATE)
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLN A:244 , LEU A:711 , LYS A:712 , ALA A:714 , GLU A:732 , HOH A:2166
BINDING SITE FOR RESIDUE NA A 1000
2
AC2
SOFTWARE
LEU A:253 , PHE A:256 , GLN A:259 , LEU A:260 , VAL A:263 , ALA A:306 , ILE A:765 , VAL A:769 , VAL A:772 , PHE A:776 , ILE A:829 , PHE A:834 , TYR A:837 , MET A:838 , HOH A:4214
BINDING SITE FOR RESIDUE TG1 A 1003
3
AC3
SOFTWARE
THR A:353 , GLU A:439 , PHE A:487 , ARG A:489 , LYS A:515 , ARG A:560 , LEU A:562 , GLY A:626 , ARG A:678 , HOH A:2012 , HOH A:4237 , HOH A:4267 , HOH A:4276 , HOH A:4277 , HOH A:4296
BINDING SITE FOR RESIDUE TM1 A 1002
4
AC4
SOFTWARE
ASN A:101 , GLN A:108 , ALA A:313 , THR A:316
BINDING SITE FOR RESIDUE PTY A 1011
5
AC5
SOFTWARE
ILE A:274 , ASN A:275 , ALA A:780 , MET A:923 , TRP A:928
BINDING SITE FOR RESIDUE PTY A 1013
6
AC6
SOFTWARE
SER A:921 , MET A:923 , GLU A:982 , PHE A:986 , ARG A:989 , ASN A:990
BINDING SITE FOR RESIDUE PTY A 1012
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: ATPASE_E1_E2 (A:351-357)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ATPASE_E1_E2
PS00154
E1-E2 ATPases phosphorylation site.
AT2A1_RABIT
351-357
1
A:351-357
[
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
(4, 4)
Info
All SCOP Domains
1a: SCOP_d3ar5a2 (A:125-239)
2a: SCOP_d3ar5a4 (A:361-599)
3a: SCOP_d3ar5a3 (A:344-360,A:600-750)
4a: SCOP_d3ar5a1 (A:1-124,A:240-343,A:751-994)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Double-stranded beta-helix
(580)
Superfamily
:
Calcium ATPase, transduction domain A
(37)
Family
:
Calcium ATPase, transduction domain A
(37)
Protein domain
:
Calcium ATPase, transduction domain A
(37)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(37)
1a
d3ar5a2
A:125-239
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Metal cation-transporting ATPase, ATP-binding domain N
(45)
Superfamily
:
Metal cation-transporting ATPase, ATP-binding domain N
(45)
Family
:
Metal cation-transporting ATPase, ATP-binding domain N
(45)
Protein domain
:
Calcium ATPase
(37)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(37)
2a
d3ar5a4
A:361-599
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
HAD-like
(349)
Superfamily
:
HAD-like
(349)
Family
:
Meta-cation ATPase, catalytic domain P
(38)
Protein domain
:
Calcium ATPase, catalytic domain P
(37)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(37)
3a
d3ar5a3
A:344-360,A:600-750
Class
:
Membrane and cell surface proteins and peptides
(2046)
Fold
:
Calcium ATPase, transmembrane domain M
(37)
Superfamily
:
Calcium ATPase, transmembrane domain M
(37)
Family
:
Calcium ATPase, transmembrane domain M
(37)
Protein domain
:
Calcium ATPase, transmembrane domain M
(37)
Rabbit (Oryctolagus cuniculus) [TaxId: 9986]
(37)
4a
d3ar5a1
A:1-124,A:240-343,A:751-994
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (335 KB)
Header - Asym.Unit
Biol.Unit 1 (328 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
3AR5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help