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3ECN
Asym. Unit
Info
Asym.Unit (119 KB)
Biol.Unit 1 (59 KB)
Biol.Unit 2 (59 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PDE8A CATALYTIC DOMAIN IN COMPLEX WITH IBMX
Authors
:
H. Wang, Z. Yan, S. Yang, J. Cai, H. Robinson, H. Ke
Date
:
01 Sep 08 (Deposition) - 25 Nov 08 (Release) - 17 Mar 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Ibmx, Pde8A Catalytic Domain, Refolding, Alternative Splicing, Camp, Hydrolase, Magnesium, Manganese, Metal- Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Wang, Z. Yan, S. Yang, J. Cai, H. Robinson, H. Ke
Kinetic And Structural Studies Of Phosphodiesterase-8A And Implication On The Inhibitor Selectivity
Biochemistry V. 47 12760 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: 3-ISOBUTYL-1-METHYLXANTHINE (IBMa)
1b: 3-ISOBUTYL-1-METHYLXANTHINE (IBMb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IBM
2
Ligand/Ion
3-ISOBUTYL-1-METHYLXANTHINE
2
MG
2
Ligand/Ion
MAGNESIUM ION
3
ZN
2
Ligand/Ion
ZINC ION
[
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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
MET A:670 , ILE A:744 , TYR A:748 , PHE A:767 , GLN A:778 , PHE A:781 , PHE A:785 , HOH A:884
BINDING SITE FOR RESIDUE IBM A 3
2
AC2
SOFTWARE
HOH B:126 , MET B:670 , ILE B:744 , TYR B:748 , GLN B:778 , PHE B:781 , PHE B:785
BINDING SITE FOR RESIDUE IBM B 3
3
AC3
SOFTWARE
HIS A:560 , HIS A:596 , ASP A:597 , ASP A:726 , HOH A:820 , HOH A:821
BINDING SITE FOR RESIDUE ZN A 1
4
AC4
SOFTWARE
ASP A:597 , HOH A:820 , HOH A:822 , HOH A:823 , HOH A:824 , HOH A:825
BINDING SITE FOR RESIDUE MG A 2
5
AC5
SOFTWARE
HOH B:11 , HOH B:12 , HIS B:560 , HIS B:596 , ASP B:597 , ASP B:726
BINDING SITE FOR RESIDUE ZN B 1
6
AC6
SOFTWARE
HOH B:11 , HOH B:13 , HOH B:14 , HOH B:15 , HOH B:16 , ASP B:597
BINDING SITE FOR RESIDUE MG B 2
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:596-607,B:596-607)
;
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.
PDE8A_HUMAN
596-607
2
A:596-607
B:596-607
[
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Exons
(7, 14)
Info
All Exons
Exon 1.18 (A:482-512 | B:482-512)
Exon 1.19 (A:512-578 | B:512-578)
Exon 1.20 (A:579-651 | B:579-651)
Exon 1.21 (A:651-695 | B:651-695)
Exon 1.22 (A:696-751 | B:696-751)
Exon 1.23 (A:752-795 | B:752-795)
Exon 1.24b (A:795-819 | B:795-819)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.17/1.18
2: Boundary 1.18/1.19
3: Boundary 1.19/1.20
4: Boundary 1.20/1.21
5: Boundary 1.21/1.22
6: Boundary 1.22/1.23
7: Boundary 1.23/1.24b
8: Boundary 1.24b/-
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
1.2a
ENST00000394553
2a
ENSE00001655579
chr15:
85525205-85525579
375
PDE8A_HUMAN
1-62
62
0
-
-
1.3
ENST00000394553
3
ENSE00001764359
chr15:
85607601-85607657
57
PDE8A_HUMAN
63-81
19
0
-
-
1.4
ENST00000394553
4
ENSE00001636622
chr15:
85610245-85610435
191
PDE8A_HUMAN
82-145
64
0
-
-
1.5
ENST00000394553
5
ENSE00001618381
chr15:
85619093-85619149
57
PDE8A_HUMAN
145-164
20
0
-
-
1.6
ENST00000394553
6
ENSE00001684152
chr15:
85619964-85620018
55
PDE8A_HUMAN
164-182
19
0
-
-
1.7
ENST00000394553
7
ENSE00001755447
chr15:
85626787-85626875
89
PDE8A_HUMAN
183-212
30
0
-
-
1.8
ENST00000394553
8
ENSE00001695435
chr15:
85632569-85632647
79
PDE8A_HUMAN
212-238
27
0
-
-
1.10
ENST00000394553
10
ENSE00001726628
chr15:
85634275-85634412
138
PDE8A_HUMAN
239-284
46
0
-
-
1.11
ENST00000394553
11
ENSE00001601720
chr15:
85641179-85641267
89
PDE8A_HUMAN
285-314
30
0
-
-
1.12
ENST00000394553
12
ENSE00001104439
chr15:
85643246-85643297
52
PDE8A_HUMAN
314-331
18
0
-
-
1.13
ENST00000394553
13
ENSE00001104423
chr15:
85643387-85643429
43
PDE8A_HUMAN
332-346
15
0
-
-
1.14
ENST00000394553
14
ENSE00001104415
chr15:
85652284-85652361
78
PDE8A_HUMAN
346-372
27
0
-
-
1.15
ENST00000394553
15
ENSE00001104468
chr15:
85656608-85656678
71
PDE8A_HUMAN
372-395
24
0
-
-
1.16
ENST00000394553
16
ENSE00001104402
chr15:
85657104-85657268
165
PDE8A_HUMAN
396-450
55
0
-
-
1.17
ENST00000394553
17
ENSE00001104405
chr15:
85658670-85658718
49
PDE8A_HUMAN
451-467
17
0
-
-
1.18
ENST00000394553
18
ENSE00001225334
chr15:
85659215-85659350
136
PDE8A_HUMAN
467-512
46
2
A:482-512
B:482-512
31
31
1.19
ENST00000394553
19
ENSE00001104432
chr15:
85660872-85661070
199
PDE8A_HUMAN
512-578
67
2
A:512-578
B:512-578
67
67
1.20
ENST00000394553
20
ENSE00001104459
chr15:
85664028-85664245
218
PDE8A_HUMAN
579-651
73
2
A:579-651
B:579-651
73
73
1.21
ENST00000394553
21
ENSE00001104456
chr15:
85666292-85666424
133
PDE8A_HUMAN
651-695
45
2
A:651-695
B:651-695
45
45
1.22
ENST00000394553
22
ENSE00001104435
chr15:
85669438-85669605
168
PDE8A_HUMAN
696-751
56
2
A:696-751
B:696-751
56
56
1.23
ENST00000394553
23
ENSE00001104452
chr15:
85679765-85679894
130
PDE8A_HUMAN
752-795
44
2
A:752-795
B:752-795
44
44
1.24b
ENST00000394553
24b
ENSE00001370034
chr15:
85681028-85682367
1340
PDE8A_HUMAN
795-829
35
2
A:795-819
B:795-819
25
25
[
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SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d3ecna_ (A:)
1b: SCOP_d3ecnb_ (B:)
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Protein Domains
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(
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Organisms
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(
)
Class
:
All alpha proteins
(14657)
Fold
:
HD-domain/PDEase-like
(204)
Superfamily
:
HD-domain/PDEase-like
(204)
Family
:
automated matches
(60)
Protein domain
:
automated matches
(60)
Human (Homo sapiens) [TaxId: 9606]
(44)
1a
d3ecna_
A:
1b
d3ecnb_
B:
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CATH Domains
(0, 0)
Info
all CATH domains
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asym.Unit (119 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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