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1Y2E
Biol. Unit 2
Info
Asym.Unit (120 KB)
Biol.Unit 1 (59 KB)
Biol.Unit 2 (59 KB)
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(1)
Title
:
CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4D IN COMPLEX WITH 1-(4-AMINO-PHENYL)-3,5-DIMETHYL-1H-PYRAZOLE-4-CARBOXYLIC ACID ETHYL ESTER
Authors
:
G. L. Card, L. Blasdel, B. P. England, C. Zhang, Y. Suzuki, S. Gillette, D P. N. Ibrahim, D. R. Artis, G. Bollag, M. V. Milburn, S. -H. Kim, J. Schle K. Y. J. Zhang
Date
:
22 Nov 04 (Deposition) - 01 Mar 05 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Phosphodiesterase, Pde, Pde4D, Pyrazole, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. L. Card, L. Blasdel, B. P. England, C. Zhang, Y. Suzuki, S. Gillette, D. Fong, P. N. Ibrahim, D. R. Artis, G. Bollag, M. V. Milburn, S. -H. Kim, J. Schlessinger, K. Y. J. Zhang
A Family Of Phosphodiesterase Inhibitors Discovered By Cocrystallography And Scaffold-Based Drug Design
Nat. Biotechnol. V. 23 201 2005
[
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Hetero Components
(2, 7)
Info
All Hetero Components
1a: 1-(4-AMINOPHENYL)-3,5-DIMETHYL-1H-... (5DEa)
1b: 1-(4-AMINOPHENYL)-3,5-DIMETHYL-1H-... (5DEb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5DE
1
Ligand/Ion
1-(4-AMINOPHENYL)-3,5-DIMETHYL-1H-PYRAZOLE-4-CARBOXYLICACID ETHYL ESTER
2
EDO
6
Ligand/Ion
1,2-ETHANEDIOL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(10, 10)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC4 (SOFTWARE)
08: BC5 (SOFTWARE)
09: BC8 (SOFTWARE)
10: CC1 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
HIS B:164 , HIS B:200 , ASP B:201 , ASP B:318 , MG B:1002 , HOH B:2007 , HOH B:2008
BINDING SITE FOR RESIDUE ZN B 1001
02
AC4
SOFTWARE
ASP B:201 , ZN B:1001 , HOH B:2003 , HOH B:2004 , HOH B:2005 , HOH B:2006 , HOH B:2007
BINDING SITE FOR RESIDUE MG B 1002
03
AC6
SOFTWARE
HIS B:160 , MET B:273 , ASP B:318 , LEU B:319 , ASN B:321 , THR B:333 , MET B:357 , GLN B:369 , PHE B:372 , HOH B:2006 , HOH B:2060
BINDING SITE FOR RESIDUE 5DE B 1003
04
AC7
SOFTWARE
PRO A:411 , GLU B:366 , TYR B:406 , HOH B:2061
BINDING SITE FOR RESIDUE EDO B 1004
05
AC9
SOFTWARE
GLN B:327 , HOH B:2126
BINDING SITE FOR RESIDUE EDO B 1005
06
BC1
SOFTWARE
SER B:208 , PRO B:356 , CYS B:358 , HOH B:2067 , HOH B:2143
BINDING SITE FOR RESIDUE EDO B 1006
07
BC4
SOFTWARE
ARG B:257 , ARG B:261 , HOH B:2090
BINDING SITE FOR RESIDUE EDO B 417
08
BC5
SOFTWARE
ALA A:183 , GLY B:114 , ASN B:115 , ARG B:116 , HOH B:2077
BINDING SITE FOR RESIDUE EDO A 419
09
BC8
SOFTWARE
ALA B:158 , GLU B:339 , ARG B:342 , HOH B:2019 , HOH B:2072
BINDING SITE FOR RESIDUE EDO B 430
10
CC1
SOFTWARE
ASN B:115 , ALA B:155 , ASN B:162 , ILE B:163 , HOH B:2088
BINDING SITE FOR RESIDUE EDO B 434
[
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]
SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_068245 (T285P, chain B, )
2: VAR_069453 (E288A, chain B, )
3: VAR_069454 (G371D, chain B, )
4: VAR_069455 (I376T, chain B, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_068245
T
587
P
PDE4D_HUMAN
Disease (ACRDYS2)
---
B
T
285
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
B
E
288
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
B
G
371
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
B
I
376
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (B:200-211)
;
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.
PDE4D_HUMAN
502-513
1
-
B:200-211
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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, 2)
Info
All SCOP Domains
1a: SCOP_d1y2ea_ (A:)
1b: SCOP_d1y2eb_ (B:)
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Protein Domains
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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
:
Catalytic domain of cyclic nucleotide phosphodiesterase pde4d
(33)
Human (Homo sapiens) [TaxId: 9606]
(33)
1a
d1y2ea_
A:
1b
d1y2eb_
B:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1y2eA00 (A:86-411)
1b: CATH_1y2eB00 (B:88-411)
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)
Organisms
(
)
(
)
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
1y2eA00
A:86-411
1b
1y2eB00
B:88-411
[
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]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PDEase_I_1y2eB01 (B:159-403)
1b: PFAM_PDEase_I_1y2eB02 (B:159-403)
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Families
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(
)
Organisms
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)
(
)
Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-1y2eB01
B:159-403
1b
PDEase_I-1y2eB02
B:159-403
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All Atoms
Protein & NOT Variant
Protein & NOT Site
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Chain B
Asymmetric Unit 1
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Asym.Unit (120 KB)
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