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1SO2
Asym. Unit
Info
Asym.Unit (257 KB)
Biol.Unit 1 (128 KB)
Biol.Unit 2 (125 KB)
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(1)
Title
:
CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 3B IN COMPLEX WITH A DIHYDROPYRIDAZINE INHIBITOR
Authors
:
G. Scapin, S. B. Patel, C. Chung, J. P. Varnerin, S. D. Edmondson, A. Mastracchio, E. R. Parmee, J. W. Becker, S. B. Singh, L. H. Van Der Ploeg, M. R. Tota
Date
:
12 Mar 04 (Deposition) - 11 May 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Pde3B Phosphodiesterase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Scapin, S. B. Patel, C. Chung, J. P. Varnerin, S. D. Edmondson, A. Mastracchio, E. R. Parmee, S. B. Singh, J. W. Becker, L. H. Van Der Ploeg, M. R. Tota
Crystal Structure Of Human Phosphodiesterase 3B: Atomic Basis For Substrate And Inhibitor Specificity
Biochemistry V. 43 6091 2004
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 17)
Info
All Hetero Components
1a: 6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLO... (666a)
1b: 6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLO... (666b)
1c: 6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLO... (666c)
1d: 6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLO... (666d)
2a: 1-DEOXY-1-[(2-HYDROXYETHYL)(NONANO... (HG9a)
2b: 1-DEOXY-1-[(2-HYDROXYETHYL)(NONANO... (HG9b)
2c: 1-DEOXY-1-[(2-HYDROXYETHYL)(NONANO... (HG9c)
2d: 1-DEOXY-1-[(2-HYDROXYETHYL)(NONANO... (HG9d)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
666
4
Ligand/Ion
6-(4-{[2-(3-IODOBENZYL)-3-OXOCYCLOHEX-1-EN-1-YL]AMINO}PHENYL)-5-METHYL-4,5-DIHYDROPYRIDAZIN-3(2H)-ONE
2
HG9
4
Ligand/Ion
1-DEOXY-1-[(2-HYDROXYETHYL)(NONANOYL)AMINO]HEXITOL
3
MG
9
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(17, 17)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:11 , HIS A:741 , HIS A:821 , ASP A:822 , ASP A:937
BINDING SITE FOR RESIDUE MG A 471
02
AC2
SOFTWARE
HOH A:11 , HOH A:12 , HOH A:13 , HOH A:14 , HOH A:15 , ASP A:822
BINDING SITE FOR RESIDUE MG A 472
03
AC3
SOFTWARE
HOH B:21 , MG B:474 , HIS B:741 , HIS B:821 , ASP B:822 , ASP B:937
BINDING SITE FOR RESIDUE MG B 473
04
AC4
SOFTWARE
HOH B:21 , HOH B:22 , HOH B:23 , HOH B:24 , HOH B:26 , MG B:473 , ASP B:822
BINDING SITE FOR RESIDUE MG B 474
05
AC5
SOFTWARE
HOH C:31 , HIS C:741 , HIS C:821 , ASP C:822 , ASP C:937
BINDING SITE FOR RESIDUE MG C 475
06
AC6
SOFTWARE
HOH C:31 , HOH C:32 , HOH C:33 , HOH C:34 , HOH C:36 , ASP C:822
BINDING SITE FOR RESIDUE MG C 476
07
AC7
SOFTWARE
HOH D:41 , MG D:478 , HIS D:741 , HIS D:821 , ASP D:822 , ASP D:937
BINDING SITE FOR RESIDUE MG D 477
08
AC8
SOFTWARE
HOH D:41 , HOH D:42 , HOH D:43 , HOH D:44 , HOH D:46 , MG D:477 , HIS D:821 , ASP D:822
BINDING SITE FOR RESIDUE MG D 478
09
AC9
SOFTWARE
HOH A:51 , HOH A:52 , HOH A:53 , HOH A:54 , ASN A:968 , ASP B:875
BINDING SITE FOR RESIDUE MG A 479
10
BC1
SOFTWARE
HOH B:223 , HOH B:256 , HOH B:385 , HOH B:391 , ASN B:957 , ARG B:979 , LEU B:984 , ALA D:985 , ILE D:1071 , LYS D:1073
BINDING SITE FOR RESIDUE HG9 B 451
11
BC2
SOFTWARE
ALA B:985 , LYS B:1070 , ILE B:1071 , LYS B:1073 , LEU D:949 , ASN D:957 , TYR D:960 , ARG D:979 , LEU D:984
BINDING SITE FOR RESIDUE HG9 B 452
12
BC3
SOFTWARE
HOH A:126 , HOH A:301 , GLU A:953 , ASN A:957 , ARG A:979 , LEU A:984 , ARG B:783 , ALA C:985 , ILE C:1071 , LYS C:1073
BINDING SITE FOR RESIDUE HG9 A 453
13
BC4
SOFTWARE
ALA A:985 , ILE A:1071 , LYS A:1073 , HOH C:288 , ASN C:957 , ARG C:979
BINDING SITE FOR RESIDUE HG9 A 454
14
BC5
SOFTWARE
HOH A:148 , HOH A:200 , TYR A:736 , THR A:829 , ILE A:938 , GLY A:940 , PRO A:941 , HIS A:948 , TRP A:951 , THR A:952 , LEU A:987 , GLN A:988 , SER A:990 , PHE A:991
BINDING SITE FOR RESIDUE 666 A 461
15
BC6
SOFTWARE
TYR B:736 , ILE B:938 , GLY B:940 , PRO B:941 , HIS B:948 , TRP B:951 , THR B:952 , PHE B:976 , LEU B:987 , GLN B:988 , SER B:990 , PHE B:991
BINDING SITE FOR RESIDUE 666 B 462
16
BC7
SOFTWARE
HOH C:182 , TYR C:736 , THR C:829 , LEU C:895 , ILE C:938 , GLY C:940 , PRO C:941 , HIS C:948 , THR C:952 , LEU C:987 , GLN C:988 , SER C:990 , PHE C:991
BINDING SITE FOR RESIDUE 666 C 463
17
BC8
SOFTWARE
HOH D:320 , TYR D:736 , THR D:829 , ILE D:938 , GLY D:940 , PRO D:941 , HIS D:948 , TRP D:951 , THR D:952 , LEU D:987 , GLN D:988 , PHE D:991
BINDING SITE FOR RESIDUE 666 D 464
[
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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, 4)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:821-832,B:821-832,C:821-832,D:82...)
;
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.
PDE3B_HUMAN
821-832
4
A:821-832
B:821-832
C:821-832
D:821-832
[
close PROSITE info
]
Exons
(8, 32)
Info
All Exons
Exon 1.11 (A:659-698 | B:659-698 | C:659-698 ...)
Exon 1.12 (A:699-736 | B:699-736 | C:699-736 ...)
Exon 1.13 (A:736-766 | B:736-766 | C:736-774 ...)
Exon 1.14 (A:782-840 | B:782-840 | C:774-840 ...)
Exon 1.15 (A:841-908 | B:841-908 | C:841-908 ...)
Exon 1.16 (A:909-962 | B:909-962 | C:909-962 ...)
Exon 1.17 (A:963-1015 | B:963-1015 | C:963-10...)
Exon 1.18b (A:1053-1073 | B:1053-1073 | C:1053...)
View:
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Label:
All Exon Boundaries
1: Boundary 1.10/1.11
2: Boundary 1.11/1.12
3: Boundary 1.12/1.13
4: Boundary 1.13/1.14
5: Boundary 1.14/1.15
6: Boundary 1.15/1.16
7: Boundary 1.16/1.17
8: Boundary 1.17/1.18b
9: Boundary 1.18b/-
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
ENST00000282096
1a
ENSE00001262747
chr11:
14665269-14666599
1331
PDE3B_HUMAN
1-326
326
0
-
-
1.4a
ENST00000282096
4a
ENSE00001004419
chr11:
14793483-14793533
51
PDE3B_HUMAN
327-343
17
0
-
-
1.5b
ENST00000282096
5b
ENSE00001004407
chr11:
14807983-14808231
249
PDE3B_HUMAN
344-426
83
0
-
-
1.6b
ENST00000282096
6b
ENSE00001004406
chr11:
14810652-14810788
137
PDE3B_HUMAN
427-472
46
0
-
-
1.7
ENST00000282096
7
ENSE00001004411
chr11:
14825490-14825596
107
PDE3B_HUMAN
472-508
37
0
-
-
1.8
ENST00000282096
8
ENSE00001004410
chr11:
14839729-14839939
211
PDE3B_HUMAN
508-578
71
0
-
-
1.9b
ENST00000282096
9b
ENSE00001004414
chr11:
14840682-14840755
74
PDE3B_HUMAN
578-603
26
0
-
-
1.10
ENST00000282096
10
ENSE00001004408
chr11:
14852244-14852392
149
PDE3B_HUMAN
603-652
50
0
-
-
1.11
ENST00000282096
11
ENSE00001004417
chr11:
14853186-14853323
138
PDE3B_HUMAN
653-698
46
4
A:659-698
B:659-698
C:659-698
D:659-698
40
40
40
40
1.12
ENST00000282096
12
ENSE00001004418
chr11:
14854268-14854379
112
PDE3B_HUMAN
699-736
38
4
A:699-736
B:699-736
C:699-736
D:699-736
38
38
38
38
1.13
ENST00000282096
13
ENSE00001004415
chr11:
14856528-14856641
114
PDE3B_HUMAN
736-774
39
4
A:736-766
B:736-766
C:736-774 (gaps)
D:736-766
31
31
39
31
1.14
ENST00000282096
14
ENSE00001004409
chr11:
14865373-14865572
200
PDE3B_HUMAN
774-840
67
4
A:782-840
B:782-840
C:774-840
D:780-840
59
59
67
61
1.15
ENST00000282096
15
ENSE00001004413
chr11:
14880589-14880792
204
PDE3B_HUMAN
841-908
68
4
A:841-908
B:841-908
C:841-908
D:841-908
68
68
68
68
1.16
ENST00000282096
16
ENSE00001004416
chr11:
14882751-14882912
162
PDE3B_HUMAN
909-962
54
4
A:909-962
B:909-962
C:909-962
D:909-962
54
54
54
54
1.17
ENST00000282096
17
ENSE00001004412
chr11:
14889052-14889304
253
PDE3B_HUMAN
963-1047
85
4
A:963-1015
B:963-1015
C:963-1015
D:963-1017
53
53
53
55
1.18b
ENST00000282096
18b
ENSE00001329007
chr11:
14891007-14892350
1344
PDE3B_HUMAN
1047-1112
66
4
A:1053-1073
B:1053-1073
C:1053-1073
D:1055-1073
21
21
21
19
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1so2a_ (A:)
1b: SCOP_d1so2b_ (B:)
1c: SCOP_d1so2c_ (C:)
1d: SCOP_d1so2d_ (D:)
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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
:
cGMP-inhibited 3',5'-cyclic phosphodiesterase B, pde3b
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1so2a_
A:
1b
d1so2b_
B:
1c
d1so2c_
C:
1d
d1so2d_
D:
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CATH Domains
(0, 0)
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all CATH domains
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_PDEase_I_1so2D01 (D:798-1007)
1b: PFAM_PDEase_I_1so2D02 (D:798-1007)
1c: PFAM_PDEase_I_1so2D03 (D:798-1007)
1d: PFAM_PDEase_I_1so2D04 (D:798-1007)
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Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-1so2D01
D:798-1007
1b
PDEase_I-1so2D02
D:798-1007
1c
PDEase_I-1so2D03
D:798-1007
1d
PDEase_I-1so2D04
D:798-1007
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Asym.Unit (257 KB)
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