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1Y2K
Biol. Unit 2
Info
Asym.Unit (127 KB)
Biol.Unit 1 (62 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-(3-NITRO-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
:
1.36
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, 16)
Info
All Hetero Components
1a: 3,5-DIMETHYL-1-(3-NITROPHENYL)-1H-... (7DEa)
1b: 3,5-DIMETHYL-1-(3-NITROPHENYL)-1H-... (7DEb)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
2ae: 1,2-ETHANEDIOL (EDOae)
2af: 1,2-ETHANEDIOL (EDOaf)
2ag: 1,2-ETHANEDIOL (EDOag)
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)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
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
7DE
1
Ligand/Ion
3,5-DIMETHYL-1-(3-NITROPHENYL)-1H-PYRAZOLE-4-CARBOXYLICACID ETHYL ESTER
2
EDO
15
Ligand/Ion
1,2-ETHANEDIOL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(23, 23)
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: BC4 (SOFTWARE)
10: BC8 (SOFTWARE)
11: BC9 (SOFTWARE)
12: CC1 (SOFTWARE)
13: CC6 (SOFTWARE)
14: CC7 (SOFTWARE)
15: CC8 (SOFTWARE)
16: CC9 (SOFTWARE)
17: DC2 (SOFTWARE)
18: DC4 (SOFTWARE)
19: DC6 (SOFTWARE)
20: DC7 (SOFTWARE)
21: DC9 (SOFTWARE)
22: EC1 (SOFTWARE)
23: EC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
HIS B:164 , HIS B:200 , ASP B:201 , ASP B:318 , HOH B:2007 , HOH B:2008
BINDING SITE FOR RESIDUE ZN B 1001
02
AC4
SOFTWARE
ASP B:201 , 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 , THR B:271 , MET B:273 , ASP B:318 , LEU B:319 , ASN B:321 , THR B:333 , ILE B:336 , GLN B:369 , PHE B:372 , HOH B:2018 , HOH B:2025 , HOH B:2220
BINDING SITE FOR RESIDUE 7DE B 601
04
AC7
SOFTWARE
PRO A:411 , GLU B:366 , TYR B:406 , HOH B:2032
BINDING SITE FOR RESIDUE EDO B 701
05
AC8
SOFTWARE
LYS A:262 , ILE A:265 , ASP A:266 , HOH A:1025 , HOH B:2184
BINDING SITE FOR RESIDUE EDO A 702
06
BC1
SOFTWARE
HOH A:1088 , EDO B:728 , HOH B:2104
BINDING SITE FOR RESIDUE EDO B 706
07
BC2
SOFTWARE
GLU A:150 , ASP A:151 , TYR A:153 , ASN A:162 , HOH A:1075 , HOH A:1148 , HOH A:1204 , GLN B:407
BINDING SITE FOR RESIDUE EDO A 707
08
BC3
SOFTWARE
SER B:208 , PHE B:340 , GLN B:343 , PRO B:356
BINDING SITE FOR RESIDUE EDO B 708
09
BC4
SOFTWARE
LYS B:255 , GLN B:258 , SER B:259
BINDING SITE FOR RESIDUE EDO B 709
10
BC8
SOFTWARE
ARG B:257 , ARG B:261 , EDO B:718 , HOH B:2072 , HOH B:2110
BINDING SITE FOR RESIDUE EDO B 717
11
BC9
SOFTWARE
ARG B:257 , GLN B:258 , ARG B:261 , EDO B:717 , HOH B:2206
BINDING SITE FOR RESIDUE EDO B 718
12
CC1
SOFTWARE
ALA A:183 , VAL A:184 , HOH A:1128 , GLY B:114 , ASN B:115 , ARG B:116
BINDING SITE FOR RESIDUE EDO A 719
13
CC6
SOFTWARE
ASN A:224 , LYS B:262 , ILE B:265 , ASP B:266 , HOH B:2041
BINDING SITE FOR RESIDUE EDO B 725
14
CC7
SOFTWARE
HOH A:1108 , GLU B:150 , ASP B:151 , TYR B:153 , ASN B:162 , EDO B:734 , HOH B:2010 , HOH B:2132 , HOH B:2139 , HOH B:2167
BINDING SITE FOR RESIDUE EDO B 726
15
CC8
SOFTWARE
ASN B:402 , TRP B:405 , HOH B:2033
BINDING SITE FOR RESIDUE EDO B 727
16
CC9
SOFTWARE
ARG A:330 , EDO B:706 , HOH B:2014 , HOH B:2061 , HOH B:2219
BINDING SITE FOR RESIDUE EDO B 728
17
DC2
SOFTWARE
ASP B:156 , PRO B:205 , ARG B:342 , HOH B:2022 , HOH B:2029 , HOH B:2227
BINDING SITE FOR RESIDUE EDO B 730
18
DC4
SOFTWARE
ILE A:213 , ASN A:216 , SER A:217 , ALA A:220 , LEU A:221 , ASP A:225 , HOH A:1040 , ARG B:261
BINDING SITE FOR RESIDUE EDO A 732
19
DC6
SOFTWARE
ASN B:115 , ALA B:155 , ASN B:162 , ILE B:163 , EDO B:726 , HOH B:2114 , HOH B:2167 , HOH B:2169
BINDING SITE FOR RESIDUE EDO B 734
20
DC7
SOFTWARE
MET B:277 , LEU B:280 , ALA B:281 , LYS B:284
BINDING SITE FOR RESIDUE EDO B 735
21
DC9
SOFTWARE
ASP B:282 , MET B:286 , GLN B:308
BINDING SITE FOR RESIDUE EDO B 737
22
EC1
SOFTWARE
ASP A:397 , GLU A:400 , ASP A:401 , ARG B:108
BINDING SITE FOR RESIDUE EDO A 738
23
EC3
SOFTWARE
ASP A:151 , HIS A:152 , GLY B:371 , ASP B:374 , TYR B:375 , HOH B:2124
BINDING SITE FOR RESIDUE EDO B 740
[
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:
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_d1y2ka_ (A:)
1b: SCOP_d1y2kb_ (B:)
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(
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(
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Protein Domains
(
)
(
)
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
d1y2ka_
A:
1b
d1y2kb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1y2kA00 (A:86-411)
1b: CATH_1y2kB00 (B:86-411)
View:
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Classes
(
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(
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(
)
(
)
Homologous Superfamilies
(
)
(
)
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
1y2kA00
A:86-411
1b
1y2kB00
B:86-411
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PDEase_I_1y2kB01 (B:159-403)
1b: PFAM_PDEase_I_1y2kB02 (B:159-403)
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Select:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-1y2kB01
B:159-403
1b
PDEase_I-1y2kB02
B:159-403
[
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]
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Chain B
Asymmetric Unit 1
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