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3DYL
Asym. Unit
Info
Asym.Unit (120 KB)
Biol.Unit 1 (58 KB)
Biol.Unit 2 (58 KB)
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(1)
Title
:
HUMAN PHOSPHDIESTERASE 9 SUBSTRATE COMPLEX (ES COMPLEX)
Authors
:
S. Liu, M. N. Mansour, K. Dillman, J. Perez, D. Danley, F. Menniti
Date
:
28 Jul 08 (Deposition) - 16 Sep 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Phosphodiesterase, Enzyme Mechanism, Cgmp, Hydrolase, Manganese, Metal-Binding, Phosphoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Liu, M. N. Mansour, K. S. Dillman, J. R. Perez, D. E. Danley, P. A. Aeed S. P. Simons, P. K. Lemotte, F. S. Menniti
Structural Basis For The Catalytic Mechanism Of Human Phosphodiesterase 9.
Proc. Natl. Acad. Sci. Usa V. 105 13309 2008
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Hetero Components
(5, 7)
Info
All Hetero Components
1a: FORMIC ACID (FMTa)
2a: 3-ISOBUTYL-1-METHYLXANTHINE (IBMa)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: MANGANESE (II) ION (MNa)
4b: MANGANESE (II) ION (MNb)
5a: CYCLIC GUANOSINE MONOPHOSPHATE (PCGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
FMT
1
Ligand/Ion
FORMIC ACID
2
IBM
1
Ligand/Ion
3-ISOBUTYL-1-METHYLXANTHINE
3
MG
2
Ligand/Ion
MAGNESIUM ION
4
MN
2
Ligand/Ion
MANGANESE (II) ION
5
PCG
1
Ligand/Ion
CYCLIC GUANOSINE MONOPHOSPHATE
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:256 , HIS A:292 , ASP A:293 , ASP A:402 , HOH A:1000
BINDING SITE FOR RESIDUE MN A 901
2
AC2
SOFTWARE
ASP A:293 , HOH A:1000 , HOH A:1003 , HOH A:1004 , HOH A:1005
BINDING SITE FOR RESIDUE MG A 902
3
AC3
SOFTWARE
HOH B:0 , HIS B:256 , HIS B:292 , ASP B:293 , ASP B:402
BINDING SITE FOR RESIDUE MN B 901
4
AC4
SOFTWARE
HOH B:0 , HOH B:2 , HOH B:3 , HOH B:4 , HOH B:5 , ASP B:293
BINDING SITE FOR RESIDUE MG B 902
5
AC5
SOFTWARE
HOH A:25 , HOH A:131 , HIS A:252 , HIS A:256 , ASP A:293 , ASP A:402 , ILE A:403 , LEU A:420 , TYR A:424 , ALA A:452 , GLN A:453 , PHE A:456 , HOH A:1000 , HOH A:1003 , HOH A:1005
BINDING SITE FOR RESIDUE PCG A 900
6
AC6
SOFTWARE
ILE A:496 , MET A:500 , HOH B:28 , HOH B:36 , LEU B:420 , TYR B:424 , ALA B:452 , GLN B:453 , PHE B:456
BINDING SITE FOR RESIDUE IBM B 900
7
AC7
SOFTWARE
HOH B:0 , HOH B:2 , HOH B:33 , PHE B:251 , HIS B:252 , HIS B:256 , ASP B:293 , ASP B:402
BINDING SITE FOR RESIDUE FMT B 1
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:292-303,B:292-303)
;
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.
PDE9A_HUMAN
352-363
2
A:292-303
B:292-303
[
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Exons
(11, 22)
Info
All Exons
Exon 1.12 (A:178-185 | B:178-185)
Exon 1.13 (A:186-210 | B:186-210)
Exon 1.14b (A:211-239 | B:211-239)
Exon 1.15 (A:240-274 | B:240-274)
Exon 1.16 (A:275-302 | B:275-302)
Exon 1.17b (A:302-354 | B:302-354)
Exon 1.18 (A:355-392 | B:355-392)
Exon 1.19a (A:393-427 | B:393-427)
Exon 1.20 (A:428-470 | B:428-470)
Exon 1.21 (A:471-502 | B:471-502)
Exon 1.22 (A:503-505 | B:503-505)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.11/1.12
02: Boundary 1.12/1.13
03: Boundary 1.13/1.14b
04: Boundary 1.14b/1.15
05: Boundary 1.15/1.16
06: Boundary 1.16/1.17b
07: Boundary 1.17b/1.18
08: Boundary 1.18/1.19a
09: Boundary 1.19a/1.20
10: Boundary 1.20/1.21
11: Boundary 1.21/1.22
12: Boundary 1.22/1.23
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
1.1d
ENST00000291539
1d
ENSE00002151102
chr21:
44073865-44073993
129
PDE9A_HUMAN
1-23
23
0
-
-
1.2a
ENST00000291539
2a
ENSE00001050441
chr21:
44106302-44106372
71
PDE9A_HUMAN
24-47
24
0
-
-
1.3
ENST00000291539
3
ENSE00001747303
chr21:
44108027-44108104
78
PDE9A_HUMAN
47-73
27
0
-
-
1.5b
ENST00000291539
5b
ENSE00001592516
chr21:
44119078-44119121
44
PDE9A_HUMAN
73-88
16
0
-
-
1.8b
ENST00000291539
8b
ENSE00001792262
chr21:
44151880-44152059
180
PDE9A_HUMAN
88-148
61
0
-
-
1.9
ENST00000291539
9
ENSE00001050439
chr21:
44152180-44152234
55
PDE9A_HUMAN
148-166
19
0
-
-
1.10
ENST00000291539
10
ENSE00001050446
chr21:
44153466-44153536
71
PDE9A_HUMAN
166-190
25
0
-
-
1.11
ENST00000291539
11
ENSE00001050442
chr21:
44163886-44163970
85
PDE9A_HUMAN
190-218
29
0
-
-
1.12
ENST00000291539
12
ENSE00001292678
chr21:
44171226-44171307
82
PDE9A_HUMAN
218-245
28
2
A:178-185
B:178-185
8
8
1.13
ENST00000291539
13
ENSE00001050443
chr21:
44174100-44174174
75
PDE9A_HUMAN
246-270
25
2
A:186-210
B:186-210
25
25
1.14b
ENST00000291539
14b
ENSE00001050445
chr21:
44179109-44179195
87
PDE9A_HUMAN
271-299
29
2
A:211-239
B:211-239
29
29
1.15
ENST00000291539
15
ENSE00001050438
chr21:
44180438-44180542
105
PDE9A_HUMAN
300-334
35
2
A:240-274
B:240-274
35
35
1.16
ENST00000291539
16
ENSE00001050435
chr21:
44180935-44181017
83
PDE9A_HUMAN
335-362
28
2
A:275-302
B:275-302
28
28
1.17b
ENST00000291539
17b
ENSE00001050447
chr21:
44182193-44182349
157
PDE9A_HUMAN
362-414
53
2
A:302-354
B:302-354
53
53
1.18
ENST00000291539
18
ENSE00001050433
chr21:
44185491-44185604
114
PDE9A_HUMAN
415-452
38
2
A:355-392
B:355-392
38
38
1.19a
ENST00000291539
19a
ENSE00001050450
chr21:
44188298-44188402
105
PDE9A_HUMAN
453-487
35
2
A:393-427
B:393-427
35
35
1.20
ENST00000291539
20
ENSE00001050437
chr21:
44189137-44189265
129
PDE9A_HUMAN
488-530
43
2
A:428-470
B:428-470
43
43
1.21
ENST00000291539
21
ENSE00001309081
chr21:
44190813-44190908
96
PDE9A_HUMAN
531-562
32
2
A:471-502
B:471-502
32
32
1.22
ENST00000291539
22
ENSE00001050432
chr21:
44192549-44192630
82
PDE9A_HUMAN
563-590
28
2
A:503-505
B:503-505
3
3
1.23
ENST00000291539
23
ENSE00001851903
chr21:
44195390-44195619
230
PDE9A_HUMAN
590-593
4
0
-
-
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3dyla_ (A:)
1b: SCOP_d3dylb_ (B:)
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Protein Domains
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(
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Organisms
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(
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Class
:
All alpha proteins
(14657)
Fold
:
HD-domain/PDEase-like
(204)
Superfamily
:
HD-domain/PDEase-like
(204)
Family
:
PDEase
(118)
Protein domain
:
High-affinity cGMP-specific 3',5'-cyclic phosphodiesterase 9A, PDE9A
(16)
Human (Homo sapiens) [TaxId: 9606]
(16)
1a
d3dyla_
A:
1b
d3dylb_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3dylA00 (A:178-505)
1b: CATH_3dylB00 (B:178-505)
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Organisms
(
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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
3dylA00
A:178-505
1b
3dylB00
B:178-505
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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