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.
1TAZ
Asym. Unit
Info
Asym.Unit (65 KB)
Biol.Unit 1 (60 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 1B
Authors
:
K. Y. J. Zhang, G. L. Card, Y. Suzuki, D. R. Artis, D. Fong, S. Gillette, D. J. Neiman, B. L. West, C. Zhang, M. V. Milburn, S. -H. Kim, J. Schlessing G. Bollag
Date
:
19 May 04 (Deposition) - 03 Aug 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.77
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Pde1B, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Y. J. Zhang, G. L. Card, Y. Suzuki, D. R. Artis, D. Fong, S. Gillette, D. Hsieh, J. Neiman, B. L. West, C. Zhang, M. V. Milburn, S. -H. Kim, J. Schlessinger, G. Bollag
A Glutamine Switch Mechanism For Nucleotide Selectivity By Phosphodiesterases
Mol. Cell V. 15 279 2004
[
close entry info
]
Hetero Components
(3, 3)
Info
All Hetero Components
1a: S,S-(2-HYDROXYETHYL)THIOCYSTEINE (CMEa)
2a: MAGNESIUM ION (MGa)
3a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CME
1
Mod. Amino Acid
S,S-(2-HYDROXYETHYL)THIOCYSTEINE
2
MG
1
Ligand/Ion
MAGNESIUM ION
3
ZN
1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:227 , HIS A:263 , ASP A:264 , ASP A:370 , HOH A:1007 , HOH A:1008
BINDING SITE FOR RESIDUE ZN A 1001
2
AC2
SOFTWARE
ASP A:264 , HOH A:1003 , HOH A:1004 , HOH A:1005 , HOH A:1006 , HOH A:1007
BINDING SITE FOR RESIDUE MG A 1002
[
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: PDEASE_I (A:263-274)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PDEASE_I
PS00126
3'5'-cyclic nucleotide phosphodiesterases signature.
PDE1B_HUMAN
263-274
1
A:263-274
[
close PROSITE info
]
Exons
(10, 10)
Info
All Exons
Exon 1.6 (A:146-159)
Exon 1.7 (A:160-198)
Exon 1.8 (A:199-245)
Exon 1.9 (A:246-279)
Exon 1.10 (A:279-321)
Exon 1.11 (A:321-355 (gaps))
Exon 1.12 (A:355-395)
Exon 1.13 (A:396-423 (gaps))
Exon 1.14 (A:423-445)
Exon 1.15 (A:473-502)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.5/1.6
02: Boundary 1.6/1.7
03: Boundary 1.7/1.8
04: Boundary 1.8/1.9
05: Boundary 1.9/1.10
06: Boundary 1.10/1.11
07: Boundary 1.11/1.12
08: Boundary 1.12/1.13
09: Boundary 1.13/1.14
10: Boundary 1.14/1.15
11: Boundary 1.15/1.16
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000243052
1
ENSE00001183864
chr12:
54943404-54943556
153
PDE1B_HUMAN
-
0
0
-
-
1.2
ENST00000243052
2
ENSE00001147374
chr12:
54943644-54943769
126
PDE1B_HUMAN
1-38
38
0
-
-
1.4
ENST00000243052
4
ENSE00000838447
chr12:
54960758-54960871
114
PDE1B_HUMAN
38-76
39
0
-
-
1.5
ENST00000243052
5
ENSE00000920047
chr12:
54962968-54963150
183
PDE1B_HUMAN
76-137
62
0
-
-
1.6
ENST00000243052
6
ENSE00000920048
chr12:
54963330-54963396
67
PDE1B_HUMAN
137-159
23
1
A:146-159
14
1.7
ENST00000243052
7
ENSE00000920049
chr12:
54964025-54964141
117
PDE1B_HUMAN
160-198
39
1
A:160-198
39
1.8
ENST00000243052
8
ENSE00000920050
chr12:
54966385-54966525
141
PDE1B_HUMAN
199-245
47
1
A:199-245
47
1.9
ENST00000243052
9
ENSE00000920051
chr12:
54966932-54967032
101
PDE1B_HUMAN
246-279
34
1
A:246-279
34
1.10
ENST00000243052
10
ENSE00000920052
chr12:
54967139-54967264
126
PDE1B_HUMAN
279-321
43
1
A:279-321
43
1.11
ENST00000243052
11
ENSE00000920053
chr12:
54967392-54967493
102
PDE1B_HUMAN
321-355
35
1
A:321-355 (gaps)
35
1.12
ENST00000243052
12
ENSE00000920054
chr12:
54968882-54969002
121
PDE1B_HUMAN
355-395
41
1
A:355-395
41
1.13
ENST00000243052
13
ENSE00000920055
chr12:
54969335-54969416
82
PDE1B_HUMAN
396-423
28
1
A:396-423 (gaps)
28
1.14
ENST00000243052
14
ENSE00000920056
chr12:
54969776-54969884
109
PDE1B_HUMAN
423-459
37
1
A:423-445
23
1.15
ENST00000243052
15
ENSE00000920057
chr12:
54970355-54970485
131
PDE1B_HUMAN
459-503
45
1
A:473-502
30
1.16
ENST00000243052
16
ENSE00000920058
chr12:
54971009-54971129
121
PDE1B_HUMAN
503-536
34
0
-
-
1.17
ENST00000243052
17
ENSE00001147267
chr12:
54971644-54973023
1380
PDE1B_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1taza_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
HD-domain/PDEase-like
(204)
Superfamily
:
HD-domain/PDEase-like
(204)
Family
:
PDEase
(118)
Protein domain
:
Catalytic domain of cyclic nucleotide phosphodiesterase 1b, PDE1B
(1)
Human (Homo sapiens) [TaxId: 9606]
(1)
1a
d1taza_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1tazA00 (A:146-502)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
(66)
Homologous Superfamily
:
Catalytic domain of cyclic nucleotide phosphodiesterase 4b2b
(66)
Human (Homo sapiens)
(64)
1a
1tazA00
A:146-502
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_PDEase_I_1tazA01 (A:222-445)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-1tazA01
A:222-445
[
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 (65 KB)
Header - Asym.Unit
Biol.Unit 1 (60 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
1TAZ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help