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1XON
Biol. Unit 1
Info
Asym.Unit (128 KB)
Biol.Unit 1 (63 KB)
Biol.Unit 2 (61 KB)
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(1)
Title
:
CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4D IN COMPLEX WITH PICLAMILAST
Authors
:
G. L. Card, B. P. England, Y. Suzuki, D. Fong, B. Powell, B. Lee, C. Luu, M. Tabrizizad, S. Gillette, P. N. Ibrahim, D. R. Artis, G. Bollag, M. V. S. -H. Kim, J. Schlessinger, K. Y. J. Zhang
Date
:
06 Oct 04 (Deposition) - 14 Dec 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.72
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Phosphodiesterase, Pde, Pde4D, Piclamilast, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. L. Card, B. P. England, Y. Suzuki, D. Fong, B. Powell, B. Lee, C. Luu, M. Tabrizizad, S. Gillette, P. N. Ibrahim, D. R. Artis, G. Bollag, M. V. Milburn, S. -H. Kim, J. Schlessinger, K. Y. J. Zhang
Structural Basis For The Activity Of Drugs That Inhibit Phosphodiesterases.
Structure V. 12 2233 2004
[
close entry info
]
Hetero Components
(3, 22)
Info
All Hetero Components
1a: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHY... (B3Pa)
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)
2ah: 1,2-ETHANEDIOL (EDOah)
2ai: 1,2-ETHANEDIOL (EDOai)
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: 3-(CYCLOPENTYLOXY)-N-(3,5-DICHLORO... (PILa)
4b: 3-(CYCLOPENTYLOXY)-N-(3,5-DICHLORO... (PILb)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B3P
1
Ligand/Ion
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
2
EDO
20
Ligand/Ion
1,2-ETHANEDIOL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
PIL
1
Ligand/Ion
3-(CYCLOPENTYLOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-METHOXYBENZAMIDE
5
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(28, 28)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC1 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC7 (SOFTWARE)
10: BC8 (SOFTWARE)
11: BC9 (SOFTWARE)
12: CC1 (SOFTWARE)
13: CC3 (SOFTWARE)
14: CC4 (SOFTWARE)
15: CC5 (SOFTWARE)
16: CC6 (SOFTWARE)
17: CC7 (SOFTWARE)
18: CC8 (SOFTWARE)
19: CC9 (SOFTWARE)
20: DC1 (SOFTWARE)
21: DC3 (SOFTWARE)
22: DC4 (SOFTWARE)
23: DC6 (SOFTWARE)
24: DC8 (SOFTWARE)
25: DC9 (SOFTWARE)
26: EC1 (SOFTWARE)
27: EC3 (SOFTWARE)
28: EC4 (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
AC5
SOFTWARE
THR A:271 , MET A:273 , ASP A:318 , LEU A:319 , ASN A:321 , THR A:333 , ILE A:336 , PHE A:340 , MET A:357 , GLN A:369 , PHE A:372 , EDO A:744 , HOH A:1005 , HOH A:1010
BINDING SITE FOR RESIDUE PIL A 501
04
AC7
SOFTWARE
LYS A:94 , GLU A:95 , GLU A:97 , ASP A:98 , HIS A:105 , ARG A:108 , HOH A:1165 , HOH A:1215 , ASP B:394 , ASP B:397 , ASP B:401 , HOH B:2079
BINDING SITE FOR RESIDUE B3P A 601
05
AC9
SOFTWARE
LYS A:262 , ILE A:265 , ASP A:266 , HOH A:1037 , ASN B:224
BINDING SITE FOR RESIDUE EDO A 702
06
BC1
SOFTWARE
GLN A:210 , HOH A:1025 , HOH A:1038 , HOH A:1041
BINDING SITE FOR RESIDUE EDO A 704
07
BC3
SOFTWARE
ASN A:115 , ARG A:116 , HOH A:1123 , HOH A:1124 , ALA B:183 , VAL B:184 , HOH B:2165
BINDING SITE FOR RESIDUE EDO A 707
08
BC4
SOFTWARE
ASP A:151 , THR B:186 , ARG B:306 , EDO B:743 , HOH B:2043 , HOH B:2107
BINDING SITE FOR RESIDUE EDO A 742
09
BC7
SOFTWARE
EDO A:742 , EDO B:709
BINDING SITE FOR RESIDUE EDO B 743
10
BC8
SOFTWARE
PRO A:179 , ALA A:180 , HIS A:389 , ASP A:391 , ARG B:350
BINDING SITE FOR RESIDUE EDO A 712
11
BC9
SOFTWARE
ASN A:115 , ALA A:155 , ASN A:162 , ILE A:163 , HOH A:1086
BINDING SITE FOR RESIDUE EDO A 715
12
CC1
SOFTWARE
THR A:178 , TRP A:384 , ASP A:391 , ALA A:392 , ILE A:395 , HOH A:1114
BINDING SITE FOR RESIDUE EDO A 716
13
CC3
SOFTWARE
HOH A:1202 , ARG B:257 , GLN B:258 , ARG B:261 , EDO B:717
BINDING SITE FOR RESIDUE EDO B 718
14
CC4
SOFTWARE
VAL A:184 , LEU A:298 , LEU A:299 , LEU A:300 , ARG A:306
BINDING SITE FOR RESIDUE EDO A 719
15
CC5
SOFTWARE
PHE A:238 , ARG A:257 , ARG A:261 , HOH A:1138
BINDING SITE FOR RESIDUE EDO A 720
16
CC6
SOFTWARE
SER A:208 , PHE A:340 , PRO A:356 , HOH A:1106 , HOH A:1216
BINDING SITE FOR RESIDUE EDO A 722
17
CC7
SOFTWARE
ASP A:156 , VAL A:157 , ALA A:158 , GLU A:339 , ARG A:342 , HOH A:1040 , HOH A:1161
BINDING SITE FOR RESIDUE EDO A 745
18
CC8
SOFTWARE
MET A:273 , PHE A:372 , ILE A:376 , PIL A:501 , EDO A:723 , HOH A:1095
BINDING SITE FOR RESIDUE EDO A 744
19
CC9
SOFTWARE
ILE A:376 , EDO A:744 , HOH A:1145
BINDING SITE FOR RESIDUE EDO A 723
20
DC1
SOFTWARE
MET A:222 , HOH A:1020
BINDING SITE FOR RESIDUE EDO A 724
21
DC3
SOFTWARE
GLN A:407 , GLU B:150 , ASP B:151 , TYR B:153 , ALA B:155 , ASN B:162 , HOH B:2115
BINDING SITE FOR RESIDUE EDO B 726
22
DC4
SOFTWARE
GLN A:327 , HOH A:1081 , TRP B:405 , EDO B:728 , HOH B:2093
BINDING SITE FOR RESIDUE EDO B 727
23
DC6
SOFTWARE
ASP A:151 , HIS A:152 , TYR A:153 , HOH A:1015 , ASP B:301 , HOH B:2024 , HOH B:2107
BINDING SITE FOR RESIDUE EDO A 729
24
DC8
SOFTWARE
GLY A:371 , ASP A:374 , TYR A:375 , HOH A:1116 , ASP B:151 , HIS B:152
BINDING SITE FOR RESIDUE EDO A 731
25
DC9
SOFTWARE
ILE A:213 , ASN A:216 , SER A:217 , ALA A:220 , LEU A:221 , ASP A:225 , HOH A:1202 , ARG B:261
BINDING SITE FOR RESIDUE EDO A 732
26
EC1
SOFTWARE
HIS A:154 , ASP A:203 , LEU A:219
BINDING SITE FOR RESIDUE EDO A 733
27
EC3
SOFTWARE
GLU A:338 , PHE A:341 , ASP A:345
BINDING SITE FOR RESIDUE EDO A 736
28
EC4
SOFTWARE
GLN A:327 , ARG A:330 , GLN A:331 , HOH A:1155 , HOH B:2054
BINDING SITE FOR RESIDUE EDO A 739
[
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
View:
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All Exon Boundaries
View:
Label:
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_d1xona_ (A:)
1b: SCOP_d1xonb_ (B:)
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Classes
(
)
(
)
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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
d1xona_
A:
1b
d1xonb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1xonB00 (B:86-411)
1b: CATH_1xonA00 (A:86-411)
View:
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Classes
(
)
(
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Architectures
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(
)
Topologies
(
)
(
)
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
1xonB00
B:86-411
1b
1xonA00
A:86-411
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PDEase_I_1xonB01 (B:159-403)
1b: PFAM_PDEase_I_1xonB02 (B:159-403)
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Clans
(
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(
)
Families
(
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(
)
Organisms
(
)
(
)
Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-1xonB01
B:159-403
1b
PDEase_I-1xonB02
B:159-403
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]
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Asym.Unit (128 KB)
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