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3ITU
Asym. Unit
Info
Asym.Unit (262 KB)
Biol.Unit 1 (69 KB)
Biol.Unit 2 (68 KB)
Biol.Unit 3 (65 KB)
Biol.Unit 4 (66 KB)
Biol.Unit 5 (130 KB)
Biol.Unit 6 (130 KB)
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(1)
Title
:
HPDE2A CATALYTIC DOMAIN COMPLEXED WITH IBMX
Authors
:
J. Pandit
Date
:
28 Aug 09 (Deposition) - 27 Oct 09 (Release) - 10 Nov 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.58
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: A,C (1x)
Biol. Unit 6: B,D (1x)
Keywords
:
Zn-Binding, All-Alpha-Helical, Alternative Splicing, Cgmp, Hydrolase, Membrane, Polymorphism
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Pandit, M. D. Forman, K. F. Fennell, K. S. Dillman, F. S. Menniti
Mechanism For The Allosteric Regulation Of Phosphodiesterase 2A Deduced From The X-Ray Structure Of A Near Full-Length Construct.
Proc. Natl. Acad. Sci. Usa V. 106 18225 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 12)
Info
All Hetero Components
1a: 3-ISOBUTYL-1-METHYLXANTHINE (IBMa)
1b: 3-ISOBUTYL-1-METHYLXANTHINE (IBMb)
1c: 3-ISOBUTYL-1-METHYLXANTHINE (IBMc)
1d: 3-ISOBUTYL-1-METHYLXANTHINE (IBMd)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IBM
4
Ligand/Ion
3-ISOBUTYL-1-METHYLXANTHINE
2
MG
4
Ligand/Ion
MAGNESIUM ION
3
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:6 , HIS A:660 , HIS A:696 , ASP A:697 , ASP A:808 , HOH A:922
BINDING SITE FOR RESIDUE ZN A 1
02
AC2
SOFTWARE
HOH A:2 , HOH A:3 , HOH A:4 , HOH A:5 , ASP A:697 , HOH A:922
BINDING SITE FOR RESIDUE MG A 920
03
AC3
SOFTWARE
HOH A:42 , TYR A:655 , LEU A:809 , GLN A:812 , ILE A:826 , GLN A:859 , PHE A:862 , HOH A:1271 , HOH A:1704
BINDING SITE FOR RESIDUE IBM A 999
04
AC4
SOFTWARE
HOH B:7 , HOH B:12 , HIS B:660 , HIS B:696 , ASP B:697 , ASP B:808
BINDING SITE FOR RESIDUE ZN B 2
05
AC5
SOFTWARE
HOH B:7 , HOH B:8 , HOH B:9 , HOH B:10 , HOH B:11 , ASP B:697
BINDING SITE FOR RESIDUE MG B 920
06
AC6
SOFTWARE
HOH B:60 , LEU B:809 , GLN B:812 , ILE B:826 , GLN B:859 , PHE B:862 , HOH B:1367
BINDING SITE FOR RESIDUE IBM B 999
07
AC7
SOFTWARE
HOH C:13 , HOH C:18 , HIS C:660 , HIS C:696 , ASP C:697 , ASP C:808
BINDING SITE FOR RESIDUE ZN C 3
08
AC8
SOFTWARE
HOH C:13 , HOH C:14 , HOH C:15 , HOH C:16 , HOH C:17 , ASP C:697
BINDING SITE FOR RESIDUE MG C 920
09
AC9
SOFTWARE
HOH C:31 , HIS C:656 , LEU C:809 , GLN C:812 , ILE C:826 , GLN C:859 , PHE C:862 , HOH C:1720
BINDING SITE FOR RESIDUE IBM C 999
10
BC1
SOFTWARE
HOH D:19 , HOH D:24 , HIS D:660 , HIS D:696 , ASP D:697 , ASP D:808
BINDING SITE FOR RESIDUE ZN D 4
11
BC2
SOFTWARE
HOH D:19 , HOH D:20 , HOH D:21 , HOH D:22 , HOH D:23 , ASP D:697
BINDING SITE FOR RESIDUE MG D 920
12
BC3
SOFTWARE
HOH D:113 , LEU D:809 , GLN D:812 , ILE D:826 , GLN D:859 , PHE D:862 , HOH D:1032
BINDING SITE FOR RESIDUE IBM D 999
[
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, 4)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:696-707,B:696-707,C:696-707,D:69...)
;
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.
PDE2A_HUMAN
696-707
4
A:696-707
B:696-707
C:696-707
D:696-707
[
close PROSITE info
]
Exons
(11, 44)
Info
All Exons
Exon 1.29 (A:579-617 | B:580-617 | C:590-617 ...)
Exon 1.30b (A:618-641 | B:618-641 | C:618-641 ...)
Exon 1.31 (A:641-682 | B:641-682 | C:641-682 ...)
Exon 1.32 (A:682-711 | B:682-711 | C:682-711 ...)
Exon 1.33 (A:712-727 | B:712-727 (gaps) | C:7...)
Exon 1.34 (A:728-752 | B:728-752 | C:728-752 ...)
Exon 1.35a (A:753-786 | B:753-786 | C:753-786 ...)
Exon 1.36b (A:786-823 | B:786-823 | C:786-823 ...)
Exon 1.37 (A:824-836 | B:824-836 | C:824-836 ...)
Exon 1.38 (A:837-872 | B:837-872 | C:837-872 ...)
Exon 1.40b (A:872-916 | B:872-915 | C:872-916 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.28/1.29
02: Boundary 1.29/1.30b
03: Boundary 1.30b/1.31
04: Boundary 1.31/1.32
05: Boundary 1.32/1.33
06: Boundary 1.33/1.34
07: Boundary 1.34/1.35a
08: Boundary 1.35a/1.36b
09: Boundary 1.36b/1.37
10: Boundary 1.37/1.38
11: Boundary 1.38/1.40b
12: Boundary 1.40b/-
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
1.1b
ENST00000334456
1b
ENSE00001920521
chr11:
72385463-72385181
283
PDE2A_HUMAN
1-24
24
0
-
-
1.8d
ENST00000334456
8d
ENSE00001337724
chr11:
72353370-72353298
73
PDE2A_HUMAN
24-48
25
0
-
-
1.10
ENST00000334456
10
ENSE00001337723
chr11:
72319795-72319706
90
PDE2A_HUMAN
49-78
30
0
-
-
1.11
ENST00000334456
11
ENSE00001337722
chr11:
72316270-72316182
89
PDE2A_HUMAN
79-108
30
0
-
-
1.13
ENST00000334456
13
ENSE00001337720
chr11:
72308663-72308554
110
PDE2A_HUMAN
108-145
38
0
-
-
1.14a
ENST00000334456
14a
ENSE00001337719
chr11:
72307692-72307637
56
PDE2A_HUMAN
145-163
19
0
-
-
1.15a
ENST00000334456
15a
ENSE00001337718
chr11:
72302400-72302341
60
PDE2A_HUMAN
164-183
20
0
-
-
1.16
ENST00000334456
16
ENSE00001337717
chr11:
72301624-72301471
154
PDE2A_HUMAN
184-235
52
0
-
-
1.17b
ENST00000334456
17b
ENSE00001337716
chr11:
72301288-72301236
53
PDE2A_HUMAN
235-252
18
0
-
-
1.18
ENST00000334456
18
ENSE00001337715
chr11:
72301025-72300951
75
PDE2A_HUMAN
253-277
25
0
-
-
1.19
ENST00000334456
19
ENSE00001337714
chr11:
72300836-72300795
42
PDE2A_HUMAN
278-291
14
0
-
-
1.20
ENST00000334456
20
ENSE00001337713
chr11:
72300284-72300219
66
PDE2A_HUMAN
292-313
22
0
-
-
1.21
ENST00000334456
21
ENSE00001337712
chr11:
72299958-72299828
131
PDE2A_HUMAN
314-357
44
0
-
-
1.22
ENST00000334456
22
ENSE00001337711
chr11:
72297225-72297114
112
PDE2A_HUMAN
357-394
38
0
-
-
1.23
ENST00000334456
23
ENSE00001337710
chr11:
72296637-72296598
40
PDE2A_HUMAN
395-408
14
0
-
-
1.24
ENST00000334456
24
ENSE00001337709
chr11:
72296478-72296415
64
PDE2A_HUMAN
408-429
22
0
-
-
1.25
ENST00000334456
25
ENSE00001337707
chr11:
72295988-72295916
73
PDE2A_HUMAN
429-453
25
0
-
-
1.26b
ENST00000334456
26b
ENSE00001337705
chr11:
72295772-72295595
178
PDE2A_HUMAN
454-513
60
0
-
-
1.27b
ENST00000334456
27b
ENSE00001337704
chr11:
72295357-72295245
113
PDE2A_HUMAN
513-550
38
0
-
-
1.28
ENST00000334456
28
ENSE00001337703
chr11:
72294559-72294482
78
PDE2A_HUMAN
551-576
26
0
-
-
1.29
ENST00000334456
29
ENSE00001337702
chr11:
72293610-72293488
123
PDE2A_HUMAN
577-617
41
4
A:579-617
B:580-617
C:590-617
D:590-617
39
38
28
28
1.30b
ENST00000334456
30b
ENSE00001337701
chr11:
72292991-72292921
71
PDE2A_HUMAN
618-641
24
4
A:618-641
B:618-641
C:618-641
D:618-641
24
24
24
24
1.31
ENST00000334456
31
ENSE00001337700
chr11:
72292523-72292401
123
PDE2A_HUMAN
641-682
42
4
A:641-682
B:641-682
C:641-682
D:641-682
42
42
42
42
1.32
ENST00000334456
32
ENSE00001337698
chr11:
72292017-72291930
88
PDE2A_HUMAN
682-711
30
4
A:682-711
B:682-711
C:682-711
D:682-711
30
30
30
30
1.33
ENST00000334456
33
ENSE00001337697
chr11:
72291668-72291621
48
PDE2A_HUMAN
712-727
16
4
A:712-727
B:712-727 (gaps)
C:712-727
D:712-727
16
16
16
16
1.34
ENST00000334456
34
ENSE00001337695
chr11:
72290652-72290578
75
PDE2A_HUMAN
728-752
25
4
A:728-752
B:728-752
C:728-752
D:728-752
25
25
25
25
1.35a
ENST00000334456
35a
ENSE00001337694
chr11:
72290427-72290328
100
PDE2A_HUMAN
753-786
34
4
A:753-786
B:753-786
C:753-786
D:753-786
34
34
34
34
1.36b
ENST00000334456
36b
ENSE00001337693
chr11:
72290053-72289941
113
PDE2A_HUMAN
786-823
38
4
A:786-823
B:786-823
C:786-823
D:786-823
38
38
38
38
1.37
ENST00000334456
37
ENSE00001337692
chr11:
72289558-72289520
39
PDE2A_HUMAN
824-836
13
4
A:824-836
B:824-836
C:824-836
D:824-836
13
13
13
13
1.38
ENST00000334456
38
ENSE00001337689
chr11:
72289383-72289277
107
PDE2A_HUMAN
837-872
36
4
A:837-872
B:837-872
C:837-872
D:837-872
36
36
36
36
1.40b
ENST00000334456
40b
ENSE00001836179
chr11:
72288638-72287185
1454
PDE2A_HUMAN
872-941
70
4
A:872-916
B:872-915
C:872-916
D:872-916
45
44
45
45
[
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]
SCOP Domains
(0, 0)
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CATH Domains
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all CATH domains
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Pfam Domains
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all PFAM domains
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Asym.Unit (262 KB)
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