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1XOQ
Biol. Unit 2
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 ROFLUMILAST
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
:
1.83
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Phosphodiesterase, Pde, Pde4D, Roflumilast, 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
[
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Hetero Components
(2, 13)
Info
All Hetero Components
1a: 1,2-ETHANEDIOL (EDOa)
1b: 1,2-ETHANEDIOL (EDOb)
1c: 1,2-ETHANEDIOL (EDOc)
1d: 1,2-ETHANEDIOL (EDOd)
1e: 1,2-ETHANEDIOL (EDOe)
1f: 1,2-ETHANEDIOL (EDOf)
1g: 1,2-ETHANEDIOL (EDOg)
1h: 1,2-ETHANEDIOL (EDOh)
1i: 1,2-ETHANEDIOL (EDOi)
1j: 1,2-ETHANEDIOL (EDOj)
1k: 1,2-ETHANEDIOL (EDOk)
1l: 1,2-ETHANEDIOL (EDOl)
1m: 1,2-ETHANEDIOL (EDOm)
1n: 1,2-ETHANEDIOL (EDOn)
1o: 1,2-ETHANEDIOL (EDOo)
1p: 1,2-ETHANEDIOL (EDOp)
1q: 1,2-ETHANEDIOL (EDOq)
1r: 1,2-ETHANEDIOL (EDOr)
1s: 1,2-ETHANEDIOL (EDOs)
1t: 1,2-ETHANEDIOL (EDOt)
1u: 1,2-ETHANEDIOL (EDOu)
1v: 1,2-ETHANEDIOL (EDOv)
1w: 1,2-ETHANEDIOL (EDOw)
1x: 1,2-ETHANEDIOL (EDOx)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: 3-(CYCLOPROPYLMETHOXY)-N-(3,5-DICH... (ROFa)
3b: 3-(CYCLOPROPYLMETHOXY)-N-(3,5-DICH... (ROFb)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
EDO
12
Ligand/Ion
1,2-ETHANEDIOL
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
ROF
1
Ligand/Ion
3-(CYCLOPROPYLMETHOXY)-N-(3,5-DICHLOROPYRIDIN-4-YL)-4-(DIFLUOROMETHOXY)BENZAMIDE
4
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(19, 19)
Info
All Sites
01: AC3 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC6 (SOFTWARE)
05: AC7 (SOFTWARE)
06: AC8 (SOFTWARE)
07: AC9 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC9 (SOFTWARE)
12: CC1 (SOFTWARE)
13: CC2 (SOFTWARE)
14: CC3 (SOFTWARE)
15: CC4 (SOFTWARE)
16: CC6 (SOFTWARE)
17: CC7 (SOFTWARE)
18: DC1 (SOFTWARE)
19: DC3 (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
PRO A:411 , GLU B:366 , TYR B:406 , HOH B:2051
BINDING SITE FOR RESIDUE EDO B 1003
04
AC6
SOFTWARE
LYS A:262 , ILE A:265 , ASP A:266 , HOH A:1038 , ASN B:224
BINDING SITE FOR RESIDUE EDO A 1003
05
AC7
SOFTWARE
TRP A:405 , HOH A:1085 , HOH B:2100
BINDING SITE FOR RESIDUE EDO B 1004
06
AC8
SOFTWARE
ASN A:115 , GLU A:150 , ASP A:151 , TYR A:153 , ASN A:162 , HOH A:1093 , HOH A:1123 , GLN B:407
BINDING SITE FOR RESIDUE EDO A 1004
07
AC9
SOFTWARE
SER B:208 , PRO B:356 , HOH B:2015
BINDING SITE FOR RESIDUE EDO B 1005
08
BC4
SOFTWARE
PHE B:238 , PHE B:249 , ARG B:257 , EDO B:418 , HOH B:2097
BINDING SITE FOR RESIDUE EDO B 417
09
BC5
SOFTWARE
ARG B:257 , GLN B:258 , ARG B:261 , EDO B:417 , HOH B:2163
BINDING SITE FOR RESIDUE EDO B 418
10
BC6
SOFTWARE
ALA A:183 , VAL A:184 , HOH A:1071 , ASN B:115 , ARG B:116
BINDING SITE FOR RESIDUE EDO A 419
11
BC9
SOFTWARE
ASN A:224 , LYS B:262 , ILE B:265 , ASP B:266 , HOH B:2029
BINDING SITE FOR RESIDUE EDO B 425
12
CC1
SOFTWARE
ASN B:402 , EDO B:428 , HOH B:2044
BINDING SITE FOR RESIDUE EDO B 427
13
CC2
SOFTWARE
GLU A:366 , EDO B:427
BINDING SITE FOR RESIDUE EDO B 428
14
CC3
SOFTWARE
ASP A:151 , HIS A:152 , ASP B:374 , TYR B:375 , HOH B:2105
BINDING SITE FOR RESIDUE EDO A 429
15
CC4
SOFTWARE
ASP B:156 , VAL B:157 , ALA B:158 , GLU B:339 , ARG B:342 , HOH B:2037 , HOH B:2058 , HOH B:2120
BINDING SITE FOR RESIDUE EDO B 430
16
CC6
SOFTWARE
ASN B:115 , ALA B:155 , ASN B:162 , HOH B:2055 , HOH B:2181
BINDING SITE FOR RESIDUE EDO B 434
17
CC7
SOFTWARE
MET B:273 , MET B:277 , HOH B:2063
BINDING SITE FOR RESIDUE EDO B 441
18
DC1
SOFTWARE
SER B:368 , PHE B:372 , ILE B:376 , ROF B:501
BINDING SITE FOR RESIDUE EDO B 448
19
DC3
SOFTWARE
HIS B:160 , THR B:271 , MET B:273 , ASP B:318 , LEU B:319 , ASN B:321 , PRO B:322 , TYR B:329 , TRP B:332 , THR B:333 , ILE B:336 , MET B:357 , GLN B:369 , PHE B:372 , EDO B:448 , HOH B:2005 , HOH B:2009 , HOH B:2101
BINDING SITE FOR RESIDUE ROF B 501
[
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]
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
[
close PROSITE info
]
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_d1xoqa_ (A:)
1b: SCOP_d1xoqb_ (B:)
View:
Select:
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Classes
(
)
(
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Folds
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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
d1xoqa_
A:
1b
d1xoqb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1xoqA00 (A:86-411)
1b: CATH_1xoqB00 (B:86-411)
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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
1xoqA00
A:86-411
1b
1xoqB00
B:86-411
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PDEase_I_1xoqB01 (B:159-403)
1b: PFAM_PDEase_I_1xoqB02 (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
(
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(
)
Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-1xoqB01
B:159-403
1b
PDEase_I-1xoqB02
B:159-403
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Protein & NOT Site
Protein & NOT PROSITE
Chain B
Asymmetric Unit 1
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