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.
1PJX
Asym. Unit
Info
Asym.Unit (75 KB)
Biol.Unit 1 (69 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
0.85 ANGSTROM STRUCTURE OF SQUID GANGLION DFPASE
Authors
:
J. Koepke, H. Rueterjans, C. Luecke, G. Fritzsch
Date
:
04 Jun 03 (Deposition) - 08 Jun 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
0.85
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Phosphotriesterase (Pte), Nitrogen-Calcium Coordination, Beta- Propeller, Bond-Length And Bond-Angle Restraints, Torsion Angles, Rotamer Classification, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Koepke, E. I. Scharff, C. Lucke, H. Ruterjans, G. Fritzsch
Statistical Analysis Of Crystallographic Data Obtained From Squid Ganglion Dfpase At 0. 85 A Resolution.
Acta Crystallogr. , Sect. D V. 59 1744 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(9, 24)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: 1,2-DIMETHOXYETHANE (DXEa)
2b: 1,2-DIMETHOXYETHANE (DXEb)
2c: 1,2-DIMETHOXYETHANE (DXEc)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
5a: 1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE (ME2a)
6a: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESa)
6b: 2-(N-MORPHOLINO)-ETHANESULFONIC AC... (MESb)
7a: 2-METHOXYETHANOL (MXEa)
7b: 2-METHOXYETHANOL (MXEb)
8a: DI(HYDROXYETHYL)ETHER (PEGa)
8b: DI(HYDROXYETHYL)ETHER (PEGb)
9a: TRIETHYLENE GLYCOL (PGEa)
9b: TRIETHYLENE GLYCOL (PGEb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
2
Ligand/Ion
CALCIUM ION
2
DXE
3
Ligand/Ion
1,2-DIMETHOXYETHANE
3
EDO
8
Ligand/Ion
1,2-ETHANEDIOL
4
GOL
2
Ligand/Ion
GLYCEROL
5
ME2
1
Ligand/Ion
1-ETHOXY-2-(2-METHOXYETHOXY)ETHANE
6
MES
2
Ligand/Ion
2-(N-MORPHOLINO)-ETHANESULFONIC ACID
7
MXE
2
Ligand/Ion
2-METHOXYETHANOL
8
PEG
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
9
PGE
2
Ligand/Ion
TRIETHYLENE GLYCOL
[
close Hetero Component info
]
Sites
(24, 24)
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)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLU A:21 , ASN A:120 , ASN A:175 , ASP A:229 , HOH A:502 , HOH A:524 , HOH A:604
BINDING SITE FOR RESIDUE CA A 491
02
AC2
SOFTWARE
ASP A:232 , LEU A:273 , HIS A:274 , HOH A:509 , HOH A:615 , HOH A:623
BINDING SITE FOR RESIDUE CA A 492
03
AC3
SOFTWARE
VAL A:5 , GLU A:7 , HIS A:248 , ARG A:264 , MES A:411 , HOH A:976 , HOH A:1047
BINDING SITE FOR RESIDUE ME2 A 471
04
AC4
SOFTWARE
GLU A:7 , LYS A:43 , PRO A:44 , ASN A:67 , GLY A:68 , TYR A:69 , ARG A:91 , ARG A:264 , PHE A:311 , ME2 A:471 , HOH A:508 , HOH A:628 , HOH A:728 , HOH A:1127 , HOH A:1128
BINDING SITE FOR RESIDUE MES A 411
05
AC5
SOFTWARE
GLU A:65 , VAL A:66 , THR A:102 , PHE A:103 , GLN A:258 , HOH A:598 , HOH A:687 , HOH A:1129
BINDING SITE FOR RESIDUE MES A 412
06
AC6
SOFTWARE
LYS A:57 , VAL A:167 , ASP A:168 , ILE A:211 , MXE A:451 , HOH A:859
BINDING SITE FOR RESIDUE EDO A 421
07
AC7
SOFTWARE
PHE A:86 , PHE A:124 , PHE A:158 , THR A:159 , THR A:160 , PEG A:461 , HOH A:517 , HOH A:692 , HOH A:702 , HOH A:858 , HOH A:979
BINDING SITE FOR RESIDUE EDO A 422
08
AC8
SOFTWARE
ARG A:115 , GLU A:138 , ASN A:289 , TRP A:293 , HOH A:516 , HOH A:617 , HOH A:959
BINDING SITE FOR RESIDUE EDO A 423
09
AC9
SOFTWARE
PRO A:196 , LYS A:198 , THR A:223 , HIS A:224 , PGE A:433 , HOH A:647 , HOH A:970
BINDING SITE FOR RESIDUE EDO A 424
10
BC1
SOFTWARE
HIS A:219 , ILE A:220 , PRO A:221 , GLN A:258 , HOH A:876
BINDING SITE FOR RESIDUE EDO A 425
11
BC2
SOFTWARE
MET A:148 , ASP A:184 , GLU A:225 , PHE A:314 , PGE A:433 , HOH A:581 , HOH A:890 , HOH A:906 , HOH A:1001
BINDING SITE FOR RESIDUE EDO A 426
12
BC3
SOFTWARE
GLY A:256 , GLY A:257 , GLN A:258 , LYS A:260 , PEG A:462 , HOH A:877 , HOH A:1123
BINDING SITE FOR RESIDUE EDO A 427
13
BC4
SOFTWARE
HOH A:1082 , HOH A:1125 , HOH A:1126
BINDING SITE FOR RESIDUE EDO A 428
14
BC5
SOFTWARE
MET A:148 , GLN A:172 , ASP A:184 , PRO A:196 , THR A:197 , EDO A:424 , EDO A:426 , HOH A:644 , HOH A:826 , HOH A:970 , HOH A:1102 , HOH A:1103
BINDING SITE FOR RESIDUE PGE A 433
15
BC6
SOFTWARE
ILE A:106 , PHE A:158 , GLY A:162 , GLN A:163 , MET A:164 , THR A:279 , LYS A:280 , THR A:281 , GLU A:296 , HOH A:521 , HOH A:544 , HOH A:685 , HOH A:735
BINDING SITE FOR RESIDUE PGE A 434
16
BC7
SOFTWARE
ARG A:50 , THR A:59 , LYS A:151 , TRP A:201 , LYS A:214 , MXE A:451 , MXE A:452 , HOH A:694 , HOH A:768 , HOH A:824 , HOH A:977
BINDING SITE FOR RESIDUE DXE A 441
17
BC8
SOFTWARE
TRP A:244 , LYS A:269 , HIS A:287 , GOL A:401 , HOH A:734
BINDING SITE FOR RESIDUE DXE A 442
18
BC9
SOFTWARE
PRO A:8 , LYS A:280 , GLU A:296 , TRP A:297 , PEG A:461 , HOH A:532 , HOH A:770 , HOH A:893 , HOH A:954
BINDING SITE FOR RESIDUE DXE A 443
19
CC1
SOFTWARE
LYS A:58 , THR A:59 , ASN A:213 , LYS A:214 , EDO A:421 , DXE A:441 , HOH A:569 , HOH A:768 , HOH A:859 , HOH A:923
BINDING SITE FOR RESIDUE MXE A 451
20
CC2
SOFTWARE
LYS A:151 , THR A:169 , ALA A:170 , PHE A:171 , GLU A:194 , LYS A:214 , DXE A:441 , HOH A:531 , HOH A:670 , HOH A:694
BINDING SITE FOR RESIDUE MXE A 452
21
CC3
SOFTWARE
GLU A:37 , GLY A:312 , ILE A:313 , PHE A:314 , DXE A:442 , HOH A:619
BINDING SITE FOR RESIDUE GOL A 401
22
CC4
SOFTWARE
PRO A:8 , LEU A:9 , PHE A:10 , ASP A:143 , LYS A:310 , HOH A:559 , HOH A:716 , HOH A:728
BINDING SITE FOR RESIDUE GOL A 403
23
CC5
SOFTWARE
GLN A:84 , ILE A:106 , LYS A:280 , EDO A:422 , DXE A:443 , HOH A:639 , HOH A:702 , HOH A:832 , HOH A:858
BINDING SITE FOR RESIDUE PEG A 461
24
CC6
SOFTWARE
LYS A:63 , GLU A:65 , ASP A:255 , GLY A:256 , GLY A:257 , EDO A:427 , HOH A:573 , HOH A:629 , HOH A:844
BINDING SITE FOR RESIDUE PEG A 462
[
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
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1pjxa_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
6-bladed beta-propeller
(327)
Superfamily
:
Calcium-dependent phosphotriesterase
(35)
Family
:
SGL-like
(31)
Protein domain
:
Diisopropylfluorophosphatase (phosphotriesterase, DFP)
(21)
Squid (Loligo vulgaris) [TaxId: 6622]
(21)
1a
d1pjxa_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1pjxA00 (A:1-314)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
6 Propellor
(215)
Topology
:
Neuraminidase
(215)
Homologous Superfamily
:
TolB, C-terminal domain
(42)
Loligo vulgaris. Organism_taxid: 6622.
(11)
1a
1pjxA00
A:1-314
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_SGL_1pjxA01 (A:19-302)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Beta_propeller
(192)
Family
:
SGL
(5)
Loligo vulgaris (Common European squid)
(5)
1a
SGL-1pjxA01
A:19-302
[
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 (75 KB)
Header - Asym.Unit
Biol.Unit 1 (69 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
1PJX
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help