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1XOM
Biol. Unit 2
Info
Asym.Unit (131 KB)
Biol.Unit 1 (63 KB)
Biol.Unit 2 (64 KB)
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(1)
Title
:
CATALYTIC DOMAIN OF HUMAN PHOSPHODIESTERASE 4D IN COMPLEX WITH CILOMILAST
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. Milburn, S. -H. Kim, J. Schlessinger, K. Y. J. Zhang
Date
:
06 Oct 04 (Deposition) - 14 Dec 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.55
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Phosphodiesterase, Pde, Pde4D, Cilomilast, 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
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 12)
Info
All Hetero Components
1a: CILOMILAST (CIOa)
1b: CILOMILAST (CIOb)
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)
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
CIO
1
Ligand/Ion
CILOMILAST
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: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC7 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC7 (SOFTWARE)
12: BC9 (SOFTWARE)
13: CC1 (SOFTWARE)
14: CC4 (SOFTWARE)
15: CC5 (SOFTWARE)
16: CC6 (SOFTWARE)
17: CC8 (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 2001
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 2002
03
AC5
SOFTWARE
HIS B:160 , THR B:271 , MET B:273 , LEU B:319 , ASN B:321 , ILE B:336 , MET B:337 , PHE B:340 , MET B:357 , GLN B:369 , PHE B:372 , HOH B:2005 , HOH B:2006 , HOH B:2061 , HOH B:2072
BINDING SITE FOR RESIDUE CIO B 601
04
AC7
SOFTWARE
PRO A:411 , ARG B:330 , GLU B:366 , TYR B:406 , EDO B:713
BINDING SITE FOR RESIDUE EDO B 701
05
AC9
SOFTWARE
THR A:186 , GLU A:189 , ARG A:306 , HOH A:1026 , HOH A:1066 , ASP B:151
BINDING SITE FOR RESIDUE EDO A 703
06
BC2
SOFTWARE
LEU A:326 , ARG A:330 , EDO B:706 , HOH B:2014 , HOH B:2063 , HOH B:2236
BINDING SITE FOR RESIDUE EDO B 705
07
BC3
SOFTWARE
HOH A:1069 , EDO B:705 , HOH B:2096 , HOH B:2269
BINDING SITE FOR RESIDUE EDO B 706
08
BC4
SOFTWARE
GLU A:150 , ASP A:151 , TYR A:153 , ALA A:155 , ASN A:162 , HOH A:1067 , HOH A:1130 , GLN B:407
BINDING SITE FOR RESIDUE EDO A 707
09
BC5
SOFTWARE
LYS B:255 , GLN B:258 , SER B:259 , HOH B:2219
BINDING SITE FOR RESIDUE EDO B 709
10
BC6
SOFTWARE
LEU B:92 , SER B:113 , VAL B:120 , HOH B:2216 , HOH B:2283
BINDING SITE FOR RESIDUE EDO B 710
11
BC7
SOFTWARE
SER B:208 , PHE B:340 , GLN B:343 , SER B:355 , HOH B:2188 , HOH B:2248
BINDING SITE FOR RESIDUE EDO B 711
12
BC9
SOFTWARE
ARG B:330 , THR B:333 , ASP B:334 , VAL B:365 , TYR B:406 , EDO B:701 , HOH B:2142
BINDING SITE FOR RESIDUE EDO B 713
13
CC1
SOFTWARE
TRP A:405 , HOH A:1257 , ASP B:401 , ASN B:402 , HOH B:2014 , HOH B:2260
BINDING SITE FOR RESIDUE EDO B 714
14
CC4
SOFTWARE
PHE B:238 , LEU B:241 , PHE B:249 , ARG B:257 , LEU B:260 , ARG B:261 , EDO B:718 , HOH B:2210 , HOH B:2233
BINDING SITE FOR RESIDUE EDO B 717
15
CC5
SOFTWARE
ARG B:257 , GLN B:258 , EDO B:717 , HOH B:2122
BINDING SITE FOR RESIDUE EDO B 718
16
CC6
SOFTWARE
ALA A:183 , VAL A:184 , HOH A:1073 , ASN B:115 , ARG B:116 , HOH B:2178 , HOH B:2273
BINDING SITE FOR RESIDUE EDO A 719
17
CC8
SOFTWARE
HOH B:2022 , HOH B:2183
BINDING SITE FOR RESIDUE EDO B 721
[
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)
[
close SNP/Variant info
]
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_d1xoma_ (A:)
1b: SCOP_d1xomb_ (B:)
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Classes
(
)
(
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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
d1xoma_
A:
1b
d1xomb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1xomA00 (A:86-411)
1b: CATH_1xomB00 (B:88-411)
View:
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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
1xomA00
A:86-411
1b
1xomB00
B:88-411
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PDEase_I_1xomB01 (B:159-403)
1b: PFAM_PDEase_I_1xomB02 (B:159-403)
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Clans
(
)
(
)
Families
(
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(
)
Organisms
(
)
(
)
Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-1xomB01
B:159-403
1b
PDEase_I-1xomB02
B:159-403
[
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]
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Asymmetric Unit 1
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