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3G4I
Asym. Unit
Info
Asym.Unit (249 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (63 KB)
Biol.Unit 3 (64 KB)
Biol.Unit 4 (65 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 4D WITH D155871
Authors
:
B. L. Staker
Date
:
03 Feb 09 (Deposition) - 19 Jan 10 (Release) - 19 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Phosphodiesterase, Pde4D, Alternative Splicing, Camp, Cytoplasm, Cytoskeleton, Hydrolase, Membrane, Metal- Binding, Phosphoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. B. Burgin, O. T. Magnusson, J. Singh, P. Witte, B. L. Staker, J. M. Bjornsson, M. Thorsteinsdottir, S. Hrafnsdottir, T. Hagen, A. S. Kiselyov, L. J. Stewart, M. E. Gurney
Design Of Phosphodiesterase 4D (Pde4D) Allosteric Modulators For Enhancing Cognition With Improved Safety.
Nat. Biotechnol. V. 28 63 2010
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(5, 23)
Info
All Hetero Components
1a: 1-(3-NITROPHENYL)-3-(PYRIDIN-4-YLM... (D71a)
1b: 1-(3-NITROPHENYL)-3-(PYRIDIN-4-YLM... (D71b)
1c: 1-(3-NITROPHENYL)-3-(PYRIDIN-4-YLM... (D71c)
1d: 1-(3-NITROPHENYL)-3-(PYRIDIN-4-YLM... (D71d)
2a: ETHANOL (EOHa)
2b: ETHANOL (EOHb)
2c: ETHANOL (EOHc)
2d: ETHANOL (EOHd)
2e: ETHANOL (EOHe)
2f: ETHANOL (EOHf)
2g: ETHANOL (EOHg)
2h: ETHANOL (EOHh)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
D71
4
Ligand/Ion
1-(3-NITROPHENYL)-3-(PYRIDIN-4-YLMETHYL)PYRIDO[2,3-D]PYRIMIDINE-2,4(1H,3H)-DIONE
2
EOH
8
Ligand/Ion
ETHANOL
3
MG
4
Ligand/Ion
MAGNESIUM ION
4
SO4
3
Ligand/Ion
SULFATE ION
5
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(23, 23)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:330 , HIS A:366 , ASP A:367 , ASP A:484 , HOH A:721 , HOH A:737
BINDING SITE FOR RESIDUE ZN A 801
02
AC2
SOFTWARE
ASP A:367 , HOH A:687 , HOH A:721 , HOH A:738 , HOH A:749 , HOH A:946
BINDING SITE FOR RESIDUE MG A 802
03
AC3
SOFTWARE
HIS A:271 , VAL A:272 , PHE A:273 , ARG A:274 , LEU A:494 , GLN A:497
BINDING SITE FOR RESIDUE SO4 A 3
04
AC4
SOFTWARE
HOH A:30 , HOH A:51 , TYR A:325 , HIS A:326 , LEU A:485 , ASN A:487 , THR A:499 , ILE A:502 , MET A:503 , PHE A:506 , MET A:523 , SER A:534 , GLN A:535 , PHE A:538 , HOH A:690
BINDING SITE FOR RESIDUE D71 A 901
05
AC5
SOFTWARE
LYS A:428 , ASP A:432 , HOH A:655 , HOH B:89 , HOH B:704
BINDING SITE FOR RESIDUE EOH A 5
06
AC6
SOFTWARE
THR A:314 , HIS A:318 , GLU A:409 , HOH A:709 , PHE C:377 , THR C:381
BINDING SITE FOR RESIDUE EOH A 9
07
AC7
SOFTWARE
HOH A:42 , PHE A:404 , ARG A:423 , HOH A:723
BINDING SITE FOR RESIDUE EOH A 12
08
AC8
SOFTWARE
HIS B:330 , HIS B:366 , ASP B:367 , ASP B:484 , HOH B:655 , HOH B:683
BINDING SITE FOR RESIDUE ZN B 803
09
AC9
SOFTWARE
ASP B:367 , HOH B:655 , HOH B:699 , HOH B:705 , HOH B:723 , HOH B:725
BINDING SITE FOR RESIDUE MG B 804
10
BC1
SOFTWARE
HIS B:271 , VAL B:272 , PHE B:273 , ARG B:274 , GLN B:493 , LEU B:494 , GLN B:497
BINDING SITE FOR RESIDUE SO4 B 4
11
BC2
SOFTWARE
HOH B:56 , HOH B:143 , TYR B:325 , HIS B:326 , LEU B:485 , ASN B:487 , THR B:499 , ILE B:502 , MET B:523 , SER B:534 , GLN B:535 , PHE B:538 , HOH B:657 , HOH B:914
BINDING SITE FOR RESIDUE D71 B 902
12
BC3
SOFTWARE
SER B:374 , PRO B:522
BINDING SITE FOR RESIDUE EOH B 8
13
BC4
SOFTWARE
HOH B:111 , HIS B:318 , GLU B:409 , THR D:381
BINDING SITE FOR RESIDUE EOH B 10
14
BC5
SOFTWARE
HOH A:40 , HOH A:633 , LYS B:428 , ASP B:432
BINDING SITE FOR RESIDUE EOH B 11
15
BC6
SOFTWARE
HIS C:330 , HIS C:366 , ASP C:367 , ASP C:484 , HOH C:851 , HOH C:915
BINDING SITE FOR RESIDUE ZN C 805
16
BC7
SOFTWARE
ASP C:367 , HOH C:629 , HOH C:697 , HOH C:721 , HOH C:733 , HOH C:851
BINDING SITE FOR RESIDUE MG C 806
17
BC8
SOFTWARE
HIS C:271 , VAL C:272 , PHE C:273 , ARG C:274 , LEU C:494 , GLN C:497
BINDING SITE FOR RESIDUE SO4 C 2
18
BC9
SOFTWARE
HOH C:49 , TYR C:325 , HIS C:326 , LEU C:485 , ASN C:487 , THR C:499 , ILE C:502 , MET C:503 , PHE C:506 , MET C:523 , SER C:534 , GLN C:535 , PHE C:538 , HOH C:686 , HOH C:722
BINDING SITE FOR RESIDUE D71 C 903
19
CC1
SOFTWARE
LYS C:428 , ASP C:432 , HOH D:96 , HOH D:668
BINDING SITE FOR RESIDUE EOH C 6
20
CC2
SOFTWARE
HIS D:330 , HIS D:366 , ASP D:367 , ASP D:484 , HOH D:723 , HOH D:755
BINDING SITE FOR RESIDUE ZN D 807
21
CC3
SOFTWARE
ASP D:367 , HOH D:714 , HOH D:747 , HOH D:751 , HOH D:755 , HOH D:756
BINDING SITE FOR RESIDUE MG D 808
22
CC4
SOFTWARE
HOH D:129 , HOH D:171 , TYR D:325 , HIS D:326 , LEU D:485 , ASN D:487 , THR D:499 , ILE D:502 , PHE D:506 , MET D:523 , SER D:534 , GLN D:535 , PHE D:538 , HOH D:706
BINDING SITE FOR RESIDUE D71 D 904
23
CC5
SOFTWARE
HOH C:127 , HOH C:137 , LYS D:428 , ASP D:432
BINDING SITE FOR RESIDUE EOH D 7
[
close Site info
]
SAPs(SNPs)/Variants
(4, 16)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_068245 (T451P, chain A/B/C/D, )
2: VAR_069453 (E454A, chain A/B/C/D, )
3: VAR_069454 (G537D, chain A/B/C/D, )
4: VAR_069455 (I542T, chain A/B/C/D, )
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/C/D
T
451
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B/C/D
E
454
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B/C/D
G
537
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
A/B/C/D
I
542
T
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:366-377,B:366-377,C:366-377,D:36...)
;
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
4
A:366-377
B:366-377
C:366-377
D:366-377
[
close PROSITE info
]
Exons
(8, 32)
Info
All Exons
Exon 1.34 (A:248-260 | B:253-260 | C:252-260 ...)
Exon 1.35 (A:261-293 | B:261-293 | C:261-293 ...)
Exon 1.36 (A:294-348 | B:294-348 | C:294-348 ...)
Exon 1.37 (A:349-382 | B:349-382 | C:349-382 ...)
Exon 1.38 (A:382-433 | B:382-433 | C:382-433 ...)
Exon 1.39 (A:434-474 | B:434-474 | C:434-474 ...)
Exon 1.40 (A:475-535 | B:475-535 | C:475-535 ...)
Exon 1.41j (A:536-578 | B:536-578 | C:536-578 ...)
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
4
A:248-260
B:253-260
C:252-260
D:245-260
13
8
9
16
1.35
ENST00000340635
35
ENSE00001001090
chr5:
58286729-58286631
99
PDE4D_HUMAN
397-429
33
4
A:261-293
B:261-293
C:261-293
D:261-293
33
33
33
33
1.36
ENST00000340635
36
ENSE00001001087
chr5:
58285746-58285582
165
PDE4D_HUMAN
430-484
55
4
A:294-348
B:294-348
C:294-348
D:294-348
55
55
55
55
1.37
ENST00000340635
37
ENSE00001001091
chr5:
58284419-58284320
100
PDE4D_HUMAN
485-518
34
4
A:349-382
B:349-382
C:349-382
D:349-382
34
34
34
34
1.38
ENST00000340635
38
ENSE00001175221
chr5:
58273172-58273018
155
PDE4D_HUMAN
518-569
52
4
A:382-433
B:382-433
C:382-433
D:382-433
52
52
52
52
1.39
ENST00000340635
39
ENSE00001001088
chr5:
58272299-58272177
123
PDE4D_HUMAN
570-610
41
4
A:434-474
B:434-474
C:434-474
D:434-474
41
41
41
41
1.40
ENST00000340635
40
ENSE00001698537
chr5:
58271666-58271484
183
PDE4D_HUMAN
611-671
61
4
A:475-535
B:475-535
C:475-535
D:475-535
61
61
61
61
1.41j
ENST00000340635
41j
ENSE00001989721
chr5:
58270907-58264865
6043
PDE4D_HUMAN
672-809
138
4
A:536-578
B:536-578
C:536-578
D:536-578
43
43
43
43
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3g4ia_ (A:)
1b: SCOP_d3g4ib_ (B:)
1c: SCOP_d3g4ic_ (C:)
1d: SCOP_d3g4id_ (D:)
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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
d3g4ia_
A:
1b
d3g4ib_
B:
1c
d3g4ic_
C:
1d
d3g4id_
D:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
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Label:
Sorry, no Info available
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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