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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3MF0
Asym. Unit
Info
Asym.Unit (129 KB)
Biol.Unit 1 (121 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 PDE5A GAF DOMAIN (89-518)
Authors
:
H. Wang, H. Robinson, H. Ke
Date
:
01 Apr 10 (Deposition) - 22 Sep 10 (Release) - 05 Jan 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Gaf, Cgmp Signal, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Wang, H. Robinson, H. Ke
Conformation Changes, N-Terminal Involvement, And Cgmp Signal Relay In The Phosphodiesterase-5 Gaf Domain.
J. Biol. Chem. V. 285 38149 2010
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_027776 (S181A, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_027776
S
181
A
PDE5A_HUMAN
Polymorphism
17051276
A/B
S
181
A
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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
(9, 18)
Info
All Exons
Exon 1.4 (A:102-247 (gaps) | B:101-247 (gaps...)
Exon 1.5b (A:248-277 | B:248-277)
Exon 1.6 (A:278-301 | B:278-301)
Exon 1.7 (A:302-331 | B:302-331)
Exon 1.8b (A:332-377 | B:332-377)
Exon 1.9 (A:378-394 | B:378-394)
Exon 1.10 (A:407-435 | B:409-434)
Exon 1.11a (A:446-466 | B:447-466)
Exon 1.13 (A:466-519 | B:466-520)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.4
02: Boundary 1.4/1.5b
03: Boundary 1.5b/1.6
04: Boundary 1.6/1.7
05: Boundary 1.7/1.8b
06: Boundary 1.8b/1.9
07: Boundary 1.9/1.10
08: Boundary 1.10/1.11a
09: Boundary 1.11a/1.13
10: Boundary 1.13/1.15b
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
1.1a
ENST00000354960
1a
ENSE00001851914
chr4:
120550146-120549675
472
PDE5A_HUMAN
1-51
51
0
-
-
1.4
ENST00000354960
4
ENSE00001637089
chr4:
120528452-120527864
589
PDE5A_HUMAN
51-247
197
2
A:102-247 (gaps)
B:101-247 (gaps)
146
147
1.5b
ENST00000354960
5b
ENSE00000935544
chr4:
120517767-120517678
90
PDE5A_HUMAN
248-277
30
2
A:248-277
B:248-277
30
30
1.6
ENST00000354960
6
ENSE00000970323
chr4:
120488299-120488228
72
PDE5A_HUMAN
278-301
24
2
A:278-301
B:278-301
24
24
1.7
ENST00000354960
7
ENSE00000970324
chr4:
120486565-120486476
90
PDE5A_HUMAN
302-331
30
2
A:302-331
B:302-331
30
30
1.8b
ENST00000354960
8b
ENSE00000970325
chr4:
120484125-120483988
138
PDE5A_HUMAN
332-377
46
2
A:332-377
B:332-377
46
46
1.9
ENST00000354960
9
ENSE00000970326
chr4:
120481518-120481451
68
PDE5A_HUMAN
378-400
23
2
A:378-394
B:378-394
17
17
1.10
ENST00000354960
10
ENSE00000970327
chr4:
120474901-120474793
109
PDE5A_HUMAN
400-436
37
2
A:407-435
B:409-434
29
26
1.11a
ENST00000354960
11a
ENSE00000970328
chr4:
120473792-120473705
88
PDE5A_HUMAN
437-466
30
2
A:446-466
B:447-466
21
20
1.13
ENST00000354960
13
ENSE00000935541
chr4:
120463789-120463614
176
PDE5A_HUMAN
466-524
59
2
A:466-519
B:466-520
54
55
1.15b
ENST00000354960
15b
ENSE00000935545
chr4:
120460174-120460115
60
PDE5A_HUMAN
525-544
20
0
-
-
1.18
ENST00000354960
18
ENSE00001016848
chr4:
120446850-120446704
147
PDE5A_HUMAN
545-593
49
0
-
-
1.19b
ENST00000354960
19b
ENSE00001016844
chr4:
120442215-120442090
126
PDE5A_HUMAN
594-635
42
0
-
-
1.20c
ENST00000354960
20c
ENSE00001016846
chr4:
120440294-120440200
95
PDE5A_HUMAN
636-667
32
0
-
-
1.22
ENST00000354960
22
ENSE00001016843
chr4:
120432289-120432202
88
PDE5A_HUMAN
667-696
30
0
-
-
1.23b
ENST00000354960
23b
ENSE00001016840
chr4:
120428859-120428759
101
PDE5A_HUMAN
697-730
34
0
-
-
1.24b
ENST00000354960
24b
ENSE00001016847
chr4:
120427087-120427010
78
PDE5A_HUMAN
730-756
27
0
-
-
1.25
ENST00000354960
25
ENSE00001016842
chr4:
120425754-120425691
64
PDE5A_HUMAN
756-777
22
0
-
-
1.26a
ENST00000354960
26a
ENSE00001016841
chr4:
120423810-120423736
75
PDE5A_HUMAN
778-802
25
0
-
-
1.27a
ENST00000354960
27a
ENSE00001016845
chr4:
120422408-120422325
84
PDE5A_HUMAN
803-830
28
0
-
-
1.28c
ENST00000354960
28c
ENSE00001890486
chr4:
120419893-120415550
4344
PDE5A_HUMAN
831-875
45
0
-
-
[
close EXON info
]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_GAF_3mf0B01 (B:346-503)
1b: PFAM_GAF_3mf0B02 (B:346-503)
1c: PFAM_GAF_3mf0B03 (B:346-503)
1d: PFAM_GAF_3mf0B04 (B:346-503)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GAF
(44)
Family
:
GAF
(30)
Homo sapiens (Human)
(4)
1a
GAF-3mf0B01
B:346-503
1b
GAF-3mf0B02
B:346-503
1c
GAF-3mf0B03
B:346-503
1d
GAF-3mf0B04
B:346-503
[
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
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 (129 KB)
Header - Asym.Unit
Biol.Unit 1 (121 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
3MF0
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help