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1TB7
Asym. Unit
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
[
close entry info
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Hetero Components
(5, 34)
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
2
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
27
Ligand/Ion
1,2-ETHANEDIOL
4
MG
2
Ligand/Ion
MAGNESIUM ION
5
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
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Sites
(34, 34)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
31: DC4 (SOFTWARE)
32: DC5 (SOFTWARE)
33: DC6 (SOFTWARE)
34: 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
AC3
SOFTWARE
HIS B:164 , HIS B:200 , ASP B:201 , ASP B:318 , MG B:1002 , AMP B:1003 , HOH B:1175
BINDING SITE FOR RESIDUE ZN B 1001
04
AC4
SOFTWARE
ASP B:201 , ZN B:1001 , AMP B:1003 , HOH B:1172 , HOH B:1173 , HOH B:1174 , HOH B:1175
BINDING SITE FOR RESIDUE MG B 1002
05
AC5
SOFTWARE
HIS B:160 , HIS B:164 , ASP B:201 , ASP B:318 , LEU B:319 , ASN B:321 , GLN B:369 , PHE B:372 , EDO B:543 , ZN B:1001 , MG B:1002 , HOH B:1004 , HOH B:1027 , HOH B:1104 , HOH B:1174 , HOH B:1175
BINDING SITE FOR RESIDUE AMP B 1003
06
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
07
AC7
SOFTWARE
GLU B:366 , EDO B:503
BINDING SITE FOR RESIDUE EDO B 501
08
AC8
SOFTWARE
LYS A:262 , ILE A:265 , ASP A:266 , HOH A:1021
BINDING SITE FOR RESIDUE EDO A 502
09
AC9
SOFTWARE
ARG B:330 , THR B:333 , ASP B:334 , TYR B:406 , EDO B:501 , HOH B:1165
BINDING SITE FOR RESIDUE EDO B 503
10
BC1
SOFTWARE
SER B:208 , PHE B:340 , PRO B:356 , HOH B:1059
BINDING SITE FOR RESIDUE EDO B 508
11
BC2
SOFTWARE
SER B:259 , HOH B:1056
BINDING SITE FOR RESIDUE EDO B 509
12
BC3
SOFTWARE
ASN A:115 , ALA A:155 , ASN A:162 , HOH A:1064 , HOH A:1103
BINDING SITE FOR RESIDUE EDO A 515
13
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
14
BC5
SOFTWARE
PHE B:238 , ARG B:257 , ARG B:261 , HOH B:1084 , HOH B:1093
BINDING SITE FOR RESIDUE EDO B 517
15
BC6
SOFTWARE
ALA A:183 , VAL A:184 , PHE A:185
BINDING SITE FOR RESIDUE EDO A 519
16
BC7
SOFTWARE
ARG A:257 , ARG A:261 , HOH A:1146
BINDING SITE FOR RESIDUE EDO A 520
17
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
18
BC9
SOFTWARE
SER A:208 , PRO A:356 , CYS A:358 , EDO A:521
BINDING SITE FOR RESIDUE EDO A 522
19
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
20
CC2
SOFTWARE
HOH A:1032 , GLU B:218
BINDING SITE FOR RESIDUE EDO B 524
21
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
22
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
23
CC5
SOFTWARE
HIS A:154 , ASP A:203 , PRO A:205 , LEU A:219
BINDING SITE FOR RESIDUE EDO A 533
24
CC6
SOFTWARE
ASN B:115 , ALA B:155 , ASN B:162 , ILE B:163 , EDO B:526 , HOH B:1075 , HOH B:1164
BINDING SITE FOR RESIDUE EDO B 534
25
CC7
SOFTWARE
ASN B:209 , GLU B:230 , MET B:273 , EDO B:543 , HOH B:1027
BINDING SITE FOR RESIDUE EDO B 535
26
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
27
CC9
SOFTWARE
PRO A:325 , GLN A:327 , HOH A:1055 , TRP B:405 , HOH B:1076
BINDING SITE FOR RESIDUE EDO A 537
28
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
29
DC2
SOFTWARE
ARG A:116 , MET A:147 , THR A:148 , ASP A:151
BINDING SITE FOR RESIDUE EDO A 539
30
DC3
SOFTWARE
ASP A:334 , MET A:337 , GLU A:338 , PHE A:341 , HOH A:1111
BINDING SITE FOR RESIDUE EDO A 540
31
DC4
SOFTWARE
ASP B:266 , ILE B:307 , GLN B:311 , EDO B:542 , HOH B:1106
BINDING SITE FOR RESIDUE EDO B 541
32
DC5
SOFTWARE
ASP B:266 , LEU B:269 , LYS B:275 , GLN B:311 , EDO B:541
BINDING SITE FOR RESIDUE EDO B 542
33
DC6
SOFTWARE
HIS B:160 , HIS B:204 , GLY B:206 , VAL B:207 , SER B:208 , GLU B:339 , EDO B:535 , AMP B:1003 , HOH B:1027 , HOH B:1059
BINDING SITE FOR RESIDUE EDO B 543
34
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, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_068245 (T285P, chain A/B, )
2: VAR_069453 (E288A, chain A/B, )
3: VAR_069454 (G371D, chain A/B, )
4: VAR_069455 (I376T, chain A/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)
---
A/B
T
285
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B
E
288
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B
G
371
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B
I
376
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:200-211,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
2
A:200-211
B:200-211
[
close PROSITE info
]
Exons
(8, 16)
Info
All Exons
Exon 1.34 (A:87-94 | B:86-94)
Exon 1.35 (A:95-127 | B:95-127)
Exon 1.36 (A:128-182 | B:128-182)
Exon 1.37 (A:183-216 | B:183-216)
Exon 1.38 (A:216-267 | B:216-267)
Exon 1.39 (A:268-308 (gaps) | B:268-308)
Exon 1.40 (A:309-369 | B:309-369)
Exon 1.41j (A:370-411 | B:370-411)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.33b/1.34
2: Boundary 1.34/1.35
3: Boundary 1.35/1.36
4: Boundary 1.36/1.37
5: Boundary 1.37/1.38
6: Boundary 1.38/1.39
7: Boundary 1.39/1.40
8: Boundary 1.40/1.41j
9: Boundary 1.41j/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.13a
ENST00000340635
13a
ENSE00001559328
chr5:
59189625-59188995
631
PDE4D_HUMAN
1-152
152
0
-
-
1.21b
ENST00000340635
21b
ENSE00001136096
chr5:
58511794-58511603
192
PDE4D_HUMAN
152-216
65
0
-
-
1.22
ENST00000340635
22
ENSE00001682119
chr5:
58489362-58489326
37
PDE4D_HUMAN
216-228
13
0
-
-
1.23
ENST00000340635
23
ENSE00001754547
chr5:
58481088-58481015
74
PDE4D_HUMAN
229-253
25
0
-
-
1.24
ENST00000340635
24
ENSE00001719283
chr5:
58476470-58476421
50
PDE4D_HUMAN
253-270
18
0
-
-
1.31d
ENST00000340635
31d
ENSE00001750566
chr5:
58334798-58334686
113
PDE4D_HUMAN
270-307
38
0
-
-
1.33b
ENST00000340635
33b
ENSE00000914184
chr5:
58289292-58289199
94
PDE4D_HUMAN
308-339
32
0
-
-
1.34
ENST00000340635
34
ENSE00001136103
chr5:
58287831-58287659
173
PDE4D_HUMAN
339-396
58
2
A:87-94
B:86-94
8
9
1.35
ENST00000340635
35
ENSE00001001090
chr5:
58286729-58286631
99
PDE4D_HUMAN
397-429
33
2
A:95-127
B:95-127
33
33
1.36
ENST00000340635
36
ENSE00001001087
chr5:
58285746-58285582
165
PDE4D_HUMAN
430-484
55
2
A:128-182
B:128-182
55
55
1.37
ENST00000340635
37
ENSE00001001091
chr5:
58284419-58284320
100
PDE4D_HUMAN
485-518
34
2
A:183-216
B:183-216
34
34
1.38
ENST00000340635
38
ENSE00001175221
chr5:
58273172-58273018
155
PDE4D_HUMAN
518-569
52
2
A:216-267
B:216-267
52
52
1.39
ENST00000340635
39
ENSE00001001088
chr5:
58272299-58272177
123
PDE4D_HUMAN
570-610
41
2
A:268-308 (gaps)
B:268-308
41
41
1.40
ENST00000340635
40
ENSE00001698537
chr5:
58271666-58271484
183
PDE4D_HUMAN
611-671
61
2
A:309-369
B:309-369
61
61
1.41j
ENST00000340635
41j
ENSE00001989721
chr5:
58270907-58264865
6043
PDE4D_HUMAN
672-809
138
2
A:370-411
B:370-411
42
42
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1tb7a_ (A:)
1b: SCOP_d1tb7b_ (B:)
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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:
[
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1tb7B00 (B:86-411)
1b: CATH_1tb7A00 (A:87-411)
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Organisms
(
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(
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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
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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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(
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(
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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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