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1Y2C
Biol. Unit 2
Info
Asym.Unit (124 KB)
Biol.Unit 1 (60 KB)
Biol.Unit 2 (61 KB)
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(1)
Title
:
CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4D IN COMPLEX WITH 3,5-DIMETHYL-1-PHENYL-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
:
1.67
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
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Hetero Components
(2, 14)
Info
All Hetero Components
1a: 3,5-DIMETHYL-1-PHENYL-1H-PYRAZOLE-... (3DEa)
1b: 3,5-DIMETHYL-1-PHENYL-1H-PYRAZOLE-... (3DEb)
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)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
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
3DE
1
Ligand/Ion
3,5-DIMETHYL-1-PHENYL-1H-PYRAZOLE-4-CARBOXYLIC ACIDETHYL ESTER
2
EDO
13
Ligand/Ion
1,2-ETHANEDIOL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC8 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC2 (SOFTWARE)
08: BC3 (SOFTWARE)
09: BC7 (SOFTWARE)
10: BC8 (SOFTWARE)
11: CC3 (SOFTWARE)
12: CC4 (SOFTWARE)
13: CC5 (SOFTWARE)
14: CC6 (SOFTWARE)
15: CC7 (SOFTWARE)
16: CC9 (SOFTWARE)
17: DC1 (SOFTWARE)
18: DC2 (SOFTWARE)
View:
Select:
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
AC5
SOFTWARE
TYR B:159 , MET B:273 , ASP B:318 , LEU B:319 , ASN B:321 , TRP B:332 , THR B:333 , ILE B:336 , MET B:357 , GLN B:369 , PHE B:372
BINDING SITE FOR RESIDUE 3DE B 1003
04
AC7
SOFTWARE
PRO A:411 , GLU B:366 , TYR B:406 , HOH B:2060
BINDING SITE FOR RESIDUE EDO B 501
05
AC8
SOFTWARE
LYS A:262 , ILE A:265 , ASP A:266 , HOH B:2030
BINDING SITE FOR RESIDUE EDO A 502
06
BC1
SOFTWARE
HOH B:2129
BINDING SITE FOR RESIDUE EDO B 506
07
BC2
SOFTWARE
GLU A:150 , ASP A:151 , TYR A:153 , ALA A:155 , ASN A:162 , HOH A:1076 , HOH A:1141 , GLN B:407
BINDING SITE FOR RESIDUE EDO A 507
08
BC3
SOFTWARE
SER B:208 , PRO B:356 , HOH B:2069 , HOH B:2172
BINDING SITE FOR RESIDUE EDO B 508
09
BC7
SOFTWARE
PHE B:238 , PHE B:249 , ARG B:257 , ARG B:261 , EDO B:518 , HOH B:2085
BINDING SITE FOR RESIDUE EDO B 517
10
BC8
SOFTWARE
ARG B:257 , GLN B:258 , ARG B:261 , EDO B:517 , HOH B:2170
BINDING SITE FOR RESIDUE EDO B 518
11
CC3
SOFTWARE
HOH A:1036 , LYS B:262 , ILE B:265 , ASP B:266
BINDING SITE FOR RESIDUE EDO B 525
12
CC4
SOFTWARE
HOH A:1078 , GLU B:150 , ASP B:151 , TYR B:153 , ASN B:162 , HOH B:2015 , HOH B:2084 , HOH B:2125 , HOH B:2152
BINDING SITE FOR RESIDUE EDO B 526
13
CC5
SOFTWARE
HOH A:1014 , ASP B:401 , ASN B:402 , EDO B:528 , HOH B:2144
BINDING SITE FOR RESIDUE EDO B 527
14
CC6
SOFTWARE
HOH A:1100 , EDO B:527
BINDING SITE FOR RESIDUE EDO B 528
15
CC7
SOFTWARE
ASP B:156 , VAL B:157 , ALA B:158 , GLU B:339 , ARG B:342 , HOH B:2037 , HOH B:2041
BINDING SITE FOR RESIDUE EDO B 530
16
CC9
SOFTWARE
ASN B:115 , ASN B:161 , ASN B:162 , ARG B:335 , HOH B:2077 , HOH B:2089
BINDING SITE FOR RESIDUE EDO B 534
17
DC1
SOFTWARE
ASP A:151 , HIS A:152 , ASP B:374 , TYR B:375
BINDING SITE FOR RESIDUE EDO B 540
18
DC2
SOFTWARE
GLN B:210 , HOH B:2028 , HOH B:2045 , HOH B:2046
BINDING SITE FOR RESIDUE EDO B 541
[
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 B, )
2: VAR_069453 (E288A, chain B, )
3: VAR_069454 (G371D, chain B, )
4: VAR_069455 (I376T, chain B, )
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)
---
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:
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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
[
close PROSITE info
]
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_d1y2ca_ (A:)
1b: SCOP_d1y2cb_ (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
d1y2ca_
A:
1b
d1y2cb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1y2cA00 (A:86-411)
1b: CATH_1y2cB00 (B:86-411)
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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
1y2cA00
A:86-411
1b
1y2cB00
B:86-411
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PDEase_I_1y2cB01 (B:159-403)
1b: PFAM_PDEase_I_1y2cB02 (B:159-403)
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Clans
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(
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Families
(
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(
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Organisms
(
)
(
)
Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-1y2cB01
B:159-403
1b
PDEase_I-1y2cB02
B:159-403
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Chain B
Asymmetric Unit 1
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