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1TB7
Biol. Unit 1
Info
Asym.Unit (126 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 AMP
Authors
:
K. Y. J. Zhang, G. L. Card, Y. Suzuki, D. R. Artis, D. Fong, S. Gillette, D. J. Neiman, B. L. West, C. Zhang, M. V. Milburn, S. -H. Kim, J. Schlessing G. Bollag
Date
:
19 May 04 (Deposition) - 03 Aug 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.63
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Pde4D, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Y. J. Zhang, G. L. Card, Y. Suzuki, D. R. Artis, D. Fong, S. Gillette, D. Hsieh, J. Neiman, B. L. West, C. Zhang, M. V. Milburn, S. -H. Kim, J. Schlessinger, G. Bollag
A Glutamine Switch Mechanism For Nucleotide Selectivity By Phosphodiesterases
Mol. Cell V. 15 279 2004
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Hetero Components
(3, 16)
Info
All Hetero Components
1a: ADENOSINE MONOPHOSPHATE (AMPa)
1b: ADENOSINE MONOPHOSPHATE (AMPb)
2a: 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHY... (B3Pa)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AMP
1
Ligand/Ion
ADENOSINE MONOPHOSPHATE
2
B3P
1
Ligand/Ion
2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
3
EDO
14
Ligand/Ion
1,2-ETHANEDIOL
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(21, 21)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC8 (SOFTWARE)
05: BC3 (SOFTWARE)
06: BC4 (SOFTWARE)
07: BC6 (SOFTWARE)
08: BC7 (SOFTWARE)
09: BC8 (SOFTWARE)
10: BC9 (SOFTWARE)
11: CC1 (SOFTWARE)
12: CC2 (SOFTWARE)
13: CC3 (SOFTWARE)
14: CC4 (SOFTWARE)
15: CC5 (SOFTWARE)
16: CC8 (SOFTWARE)
17: CC9 (SOFTWARE)
18: DC1 (SOFTWARE)
19: DC2 (SOFTWARE)
20: DC3 (SOFTWARE)
21: DC7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:164 , HIS A:200 , ASP A:201 , ASP A:318 , MG A:1002 , AMP A:1003 , HOH A:1190
BINDING SITE FOR RESIDUE ZN A 1001
02
AC2
SOFTWARE
ASP A:201 , ZN A:1001 , AMP A:1003 , HOH A:1187 , HOH A:1188 , HOH A:1189 , HOH A:1190
BINDING SITE FOR RESIDUE MG A 1002
03
AC6
SOFTWARE
HIS A:160 , HIS A:164 , ASP A:201 , ASP A:318 , LEU A:319 , ASN A:321 , GLN A:369 , PHE A:372 , EDO A:523 , ZN A:1001 , MG A:1002 , HOH A:1005 , HOH A:1053 , HOH A:1057 , HOH A:1105 , HOH A:1187 , HOH A:1189 , HOH A:1190
BINDING SITE FOR RESIDUE AMP A 1003
04
AC8
SOFTWARE
LYS A:262 , ILE A:265 , ASP A:266 , HOH A:1021
BINDING SITE FOR RESIDUE EDO A 502
05
BC3
SOFTWARE
ASN A:115 , ALA A:155 , ASN A:162 , HOH A:1064 , HOH A:1103
BINDING SITE FOR RESIDUE EDO A 515
06
BC4
SOFTWARE
THR A:178 , TRP A:384 , VAL A:388 , ASP A:391 , ALA A:392 , ILE A:395
BINDING SITE FOR RESIDUE EDO A 516
07
BC6
SOFTWARE
ALA A:183 , VAL A:184 , PHE A:185
BINDING SITE FOR RESIDUE EDO A 519
08
BC7
SOFTWARE
ARG A:257 , ARG A:261 , HOH A:1146
BINDING SITE FOR RESIDUE EDO A 520
09
BC8
SOFTWARE
HIS A:160 , GLY A:206 , VAL A:207 , SER A:208 , GLU A:339 , PHE A:340 , GLN A:343 , EDO A:522 , HOH A:1057
BINDING SITE FOR RESIDUE EDO A 521
10
BC9
SOFTWARE
SER A:208 , PRO A:356 , CYS A:358 , EDO A:521
BINDING SITE FOR RESIDUE EDO A 522
11
CC1
SOFTWARE
ASN A:209 , LEU A:229 , GLU A:230 , ASP A:272 , MET A:273 , AMP A:1003 , HOH A:1053 , HOH A:1056 , HOH A:1137 , HOH A:1187
BINDING SITE FOR RESIDUE EDO A 523
12
CC2
SOFTWARE
HOH A:1032 , GLU B:218
BINDING SITE FOR RESIDUE EDO B 524
13
CC3
SOFTWARE
ASN A:224 , LYS B:262 , ILE B:265 , ASP B:266 , HOH B:1011 , HOH B:1087
BINDING SITE FOR RESIDUE EDO B 525
14
CC4
SOFTWARE
GLN A:407 , GLU B:150 , ASP B:151 , TYR B:153 , ASN B:162 , EDO B:534 , HOH B:1075
BINDING SITE FOR RESIDUE EDO B 526
15
CC5
SOFTWARE
HIS A:154 , ASP A:203 , PRO A:205 , LEU A:219
BINDING SITE FOR RESIDUE EDO A 533
16
CC8
SOFTWARE
ARG A:330 , GLU A:366 , TRP A:405 , TYR A:406 , HOH A:1088 , PRO B:411
BINDING SITE FOR RESIDUE EDO A 536
17
CC9
SOFTWARE
PRO A:325 , GLN A:327 , HOH A:1055 , TRP B:405 , HOH B:1076
BINDING SITE FOR RESIDUE EDO A 537
18
DC1
SOFTWARE
THR A:186 , LEU A:188 , GLU A:189 , SER A:259 , MET A:263 , HOH A:1120
BINDING SITE FOR RESIDUE EDO A 538
19
DC2
SOFTWARE
ARG A:116 , MET A:147 , THR A:148 , ASP A:151
BINDING SITE FOR RESIDUE EDO A 539
20
DC3
SOFTWARE
ASP A:334 , MET A:337 , GLU A:338 , PHE A:341 , HOH A:1111
BINDING SITE FOR RESIDUE EDO A 540
21
DC7
SOFTWARE
LYS A:94 , GLU A:95 , GLU A:97 , ASP A:98 , HIS A:105 , ARG A:108 , HOH A:1147 , ASP B:394 , ASP B:397 , ASP B:401 , HOH B:1123
BINDING SITE FOR RESIDUE B3P A 601
[
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)
[
close SNP/Variant info
]
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_d1tb7a_ (A:)
1b: SCOP_d1tb7b_ (B:)
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Classes
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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
d1tb7a_
A:
1b
d1tb7b_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1tb7B00 (B:86-411)
1b: CATH_1tb7A00 (A:87-411)
View:
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Classes
(
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(
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Architectures
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Homologous Superfamilies
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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
1tb7B00
B:86-411
1b
1tb7A00
A:87-411
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_PDEase_I_1tb7B01 (B:159-403)
1b: PFAM_PDEase_I_1tb7B02 (B:159-403)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-1tb7B01
B:159-403
1b
PDEase_I-1tb7B02
B:159-403
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Protein & NOT Site
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Chain A
Asymmetric Unit 1
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Asym.Unit (126 KB)
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