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3G58
Biol. Unit 4
Info
Asym.Unit (251 KB)
Biol.Unit 1 (65 KB)
Biol.Unit 2 (63 KB)
Biol.Unit 3 (63 KB)
Biol.Unit 4 (67 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HUMAN PHOSPHODIESTERASE 4D WITH D155988/PMNPQ
Authors
:
B. L. Staker
Date
:
04 Feb 09 (Deposition) - 19 Jan 10 (Release) - 19 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.05
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
)
[
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Hetero Components
(2, 6)
Info
All Hetero Components
1a: 8-(3-NITROPHENYL)-6-(PYRIDIN-4-YLM... (988a)
1b: 8-(3-NITROPHENYL)-6-(PYRIDIN-4-YLM... (988b)
1c: 8-(3-NITROPHENYL)-6-(PYRIDIN-4-YLM... (988c)
1d: 8-(3-NITROPHENYL)-6-(PYRIDIN-4-YLM... (988d)
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)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
4a: SULFATE ION (SO4a)
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
988
1
Ligand/Ion
8-(3-NITROPHENYL)-6-(PYRIDIN-4-YLMETHYL)QUINOLINE
2
EDO
5
Ligand/Ion
1,2-ETHANEDIOL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
SO4
-1
Ligand/Ion
SULFATE ION
5
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(10, 10)
Info
All Sites
01: BC3 (SOFTWARE)
02: CC1 (SOFTWARE)
03: CC5 (SOFTWARE)
04: CC6 (SOFTWARE)
05: CC7 (SOFTWARE)
06: CC8 (SOFTWARE)
07: CC9 (SOFTWARE)
08: DC1 (SOFTWARE)
09: DC2 (SOFTWARE)
10: DC3 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
01
BC3
SOFTWARE
HOH B:88 , THR B:314 , HIS B:318 , GLU B:409 , HOH B:1033 , THR D:381
BINDING SITE FOR RESIDUE EDO B 3
02
CC1
SOFTWARE
LYS C:428 , ASP C:432 , HOH C:640 , HOH D:717
BINDING SITE FOR RESIDUE EDO C 5
03
CC5
SOFTWARE
HIS D:330 , HIS D:366 , ASP D:367 , ASP D:484 , HOH D:852
BINDING SITE FOR RESIDUE ZN D 624
04
CC6
SOFTWARE
ASP D:367 , HOH D:630 , HOH D:722 , HOH D:724 , HOH D:852 , HOH D:1023
BINDING SITE FOR RESIDUE MG D 625
05
CC7
SOFTWARE
MET D:439 , ASN D:487 , THR D:499 , ILE D:502 , PHE D:506 , MET D:523 , GLN D:535 , PHE D:538 , THR D:595 , PHE D:598 , GLN D:599 , HOH D:873
BINDING SITE FOR RESIDUE 988 D 904
06
CC8
SOFTWARE
HOH C:66 , HOH C:809 , LYS D:428 , ASP D:432
BINDING SITE FOR RESIDUE EDO D 2
07
CC9
SOFTWARE
SER D:374 , PRO D:522 , CYS D:524 , PHE D:598 , GLU D:601 , HOH D:654 , HOH D:873
BINDING SITE FOR RESIDUE EDO D 4
08
DC1
SOFTWARE
HIS D:271 , PHE D:273 , ARG D:274 , GLN D:493 , LEU D:494 , GLN D:497 , HOH D:1109
BINDING SITE FOR RESIDUE EDO D 11
09
DC2
SOFTWARE
ARG D:295 , ASP D:353 , ILE D:356
BINDING SITE FOR RESIDUE EDO D 14
10
DC3
SOFTWARE
HOH D:229 , PHE D:404 , ARG D:423 , ARG D:427 , HOH D:637
BINDING SITE FOR RESIDUE EDO D 15
[
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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 (T451P, chain D, )
2: VAR_069453 (E454A, chain D, )
3: VAR_069454 (G537D, chain D, )
4: VAR_069455 (I542T, chain 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)
---
D
T
451
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
D
E
454
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
D
G
537
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
D
I
542
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 (D:366-377)
;
View:
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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
-
-
-
D:366-377
[
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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, 4)
Info
All SCOP Domains
1a: SCOP_d3g58a_ (A:)
1b: SCOP_d3g58b_ (B:)
1c: SCOP_d3g58c_ (C:)
1d: SCOP_d3g58d_ (D:)
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Protein Domains
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(
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Organisms
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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
d3g58a_
A:
1b
d3g58b_
B:
1c
d3g58c_
C:
1d
d3g58d_
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
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Sorry, no Info available
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain D
Asymmetric Unit 1
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select residue range 5 to 10 in all chains
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Show PDB file:
Asym.Unit (251 KB)
Header - Asym.Unit
Biol.Unit 1 (65 KB)
Header - Biol.Unit 1
Biol.Unit 2 (63 KB)
Header - Biol.Unit 2
Biol.Unit 3 (63 KB)
Header - Biol.Unit 3
Biol.Unit 4 (67 KB)
Header - Biol.Unit 4
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