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1Y2B
Biol. Unit 1
Info
Asym.Unit (125 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (61 KB)
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(1)
Title
:
CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4D IN COMPLEX WITH 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
:
1.40
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
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: 3,5-DIMETHYL-1H-PYRAZOLE-4-CARBOXY... (DEEa)
1b: 3,5-DIMETHYL-1H-PYRAZOLE-4-CARBOXY... (DEEb)
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)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
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
DEE
1
Ligand/Ion
3,5-DIMETHYL-1H-PYRAZOLE-4-CARBOXYLIC ACID ETHYL ESTER
2
EDO
11
Ligand/Ion
1,2-ETHANEDIOL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(17, 17)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC8 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC8 (SOFTWARE)
11: BC9 (SOFTWARE)
12: CC1 (SOFTWARE)
13: CC2 (SOFTWARE)
14: CC4 (SOFTWARE)
15: CC5 (SOFTWARE)
16: CC6 (SOFTWARE)
17: CC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:164 , HIS A:200 , ASP A:201 , ASP A:318 , HOH A:1007 , HOH A:1008
BINDING SITE FOR RESIDUE ZN A 1001
02
AC2
SOFTWARE
ASP A:201 , HOH A:1003 , HOH A:1004 , HOH A:1005 , HOH A:1006 , HOH A:1007
BINDING SITE FOR RESIDUE MG A 1002
03
AC6
SOFTWARE
TYR A:159 , ASN A:321 , THR A:333 , ILE A:336 , GLN A:369 , PHE A:372
BINDING SITE FOR RESIDUE DEE A 502
04
AC7
SOFTWARE
PRO A:411 , ARG B:330 , GLU B:366 , TYR B:406 , HOH B:2058
BINDING SITE FOR RESIDUE EDO B 601
05
AC8
SOFTWARE
LYS A:262 , ILE A:265 , ASP A:266 , HOH A:1030
BINDING SITE FOR RESIDUE EDO A 602
06
BC1
SOFTWARE
ASN A:115 , GLU A:150 , ASP A:151 , TYR A:153 , ASN A:162 , EDO A:615 , HOH A:1157 , HOH A:1223 , GLN B:407
BINDING SITE FOR RESIDUE EDO A 607
07
BC3
SOFTWARE
PRO A:179 , HIS A:389 , PRO A:390 , ASP A:391
BINDING SITE FOR RESIDUE EDO A 612
08
BC4
SOFTWARE
ASN A:115 , ALA A:155 , ASN A:162 , ILE A:163 , EDO A:607 , HOH A:1157
BINDING SITE FOR RESIDUE EDO A 615
09
BC5
SOFTWARE
LEU A:175 , THR A:178 , TRP A:384 , ASP A:391 , ALA A:392 , HOH A:1134
BINDING SITE FOR RESIDUE EDO A 616
10
BC8
SOFTWARE
ALA A:183 , VAL A:184 , HOH A:1121 , GLY B:114 , ASN B:115 , ARG B:116 , HOH B:2144 , HOH B:2155
BINDING SITE FOR RESIDUE EDO A 619
11
BC9
SOFTWARE
PHE A:238 , PHE A:249 , ARG A:257 , ARG A:261 , HOH A:1168
BINDING SITE FOR RESIDUE EDO A 620
12
CC1
SOFTWARE
SER A:208 , PHE A:340 , PRO A:356 , HOH A:1057
BINDING SITE FOR RESIDUE EDO A 622
13
CC2
SOFTWARE
GLU A:218 , HOH B:2025
BINDING SITE FOR RESIDUE EDO A 624
14
CC4
SOFTWARE
HOH A:1009 , ASP B:401 , ASN B:402 , HOH B:2114
BINDING SITE FOR RESIDUE EDO B 627
15
CC5
SOFTWARE
GLU A:366 , HOH A:1070
BINDING SITE FOR RESIDUE EDO B 628
16
CC6
SOFTWARE
ASP A:151 , HIS A:152 , GLY B:371 , ASP B:374 , TYR B:375 , HOH B:2100 , HOH B:2192
BINDING SITE FOR RESIDUE EDO A 629
17
CC7
SOFTWARE
HIS A:154 , ASP A:203 , PRO A:205
BINDING SITE FOR RESIDUE EDO A 633
[
close Site info
]
SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_068245 (T285P, chain A, )
2: VAR_069453 (E288A, chain A, )
3: VAR_069454 (G371D, chain A, )
4: VAR_069455 (I376T, chain A, )
View:
Select:
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)
---
A
T
285
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
A
E
288
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
A
G
371
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
A
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 (A: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
A: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_d1y2ba_ (A:)
1b: SCOP_d1y2bb_ (B:)
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Protein Domains
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(
)
Organisms
(
)
(
)
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
d1y2ba_
A:
1b
d1y2bb_
B:
[
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]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1y2bA00 (A:86-411)
1b: CATH_1y2bB00 (B:86-411)
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Classes
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(
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)
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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
1y2bA00
A:86-411
1b
1y2bB00
B:86-411
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PDEase_I_1y2bB01 (B:159-403)
1b: PFAM_PDEase_I_1y2bB02 (B:159-403)
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Families
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(
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Organisms
(
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(
)
Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-1y2bB01
B:159-403
1b
PDEase_I-1y2bB02
B:159-403
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(currently selected atoms:
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Asymmetric Unit 1
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