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1SO2
Biol. Unit 1
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
)
[
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Hetero Components
(2, 6)
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
2
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
-1
Ligand/Ion
MAGNESIUM ION
[
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Sites
(11, 11)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC4 (SOFTWARE)
10: BC5 (SOFTWARE)
11: BC6 (SOFTWARE)
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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
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
06
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
07
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
08
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
09
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
10
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
11
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
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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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:821-832,B:821-832)
;
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
2
A:821-832
B:821-832
-
-
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Exons
(0, 0)
Info
All Exons
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
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)
Info
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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Show PDB file:
Asym.Unit (257 KB)
Header - Asym.Unit
Biol.Unit 1 (128 KB)
Header - Biol.Unit 1
Biol.Unit 2 (125 KB)
Header - Biol.Unit 2
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