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3JWR
Asym. Unit
Info
Asym.Unit (122 KB)
Biol.Unit 1 (60 KB)
Biol.Unit 2 (61 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CHIMERIC PDE5/PDE6 CATALYTIC DOMAIN COMPLEXED WITH 3-ISOBUTYL-1-METHYLXANTHINE (IBMX) AND PDE6 GAMMA-SUBUNIT INHIBITORY PEPTIDE 70-87.
Authors
:
B. Barren, L. Gakhar, H. Muradov, K. K. Boyd, S. Ramaswamy, N. O. Artemyev
Date
:
18 Sep 09 (Deposition) - 13 Oct 09 (Release) - 01 Dec 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.99
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Mostly Alpha, Cgmp, Hydrolase, Polymorphism, Sensory Transduction, Vision
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. Barren, L. Gakhar, H. Muradov, K. K. Boyd, S. Ramaswamy, N. O. Artemyev
Structural Basis Of Phosphodiesterase 6 Inhibition By The C-Terminal Region Of The Gamma-Subunit
Embo J. V. 28 3613 2009
(for further references see the
PDB file header
)
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: 3-ISOBUTYL-1-METHYLXANTHINE (IBMa)
1b: 3-ISOBUTYL-1-METHYLXANTHINE (IBMb)
1c: 3-ISOBUTYL-1-METHYLXANTHINE (IBMc)
1d: 3-ISOBUTYL-1-METHYLXANTHINE (IBMd)
1e: 3-ISOBUTYL-1-METHYLXANTHINE (IBMe)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IBM
5
Ligand/Ion
3-ISOBUTYL-1-METHYLXANTHINE
2
MG
2
Ligand/Ion
MAGNESIUM ION
3
ZN
2
Ligand/Ion
ZINC ION
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HIS A:617 , HIS A:653 , ASP A:654 , ASP A:764
BINDING SITE FOR RESIDUE ZN A 899
2
AC2
SOFTWARE
HOH B:12 , HOH B:18 , HIS B:617 , HIS B:653 , ASP B:654 , ASP B:764
BINDING SITE FOR RESIDUE ZN B 899
3
AC3
SOFTWARE
HOH A:5 , ASP A:654 , GLU A:682 , THR A:723
BINDING SITE FOR RESIDUE MG A 900
4
AC4
SOFTWARE
HIS A:613 , LEU A:765 , GLN A:817 , PHE A:820
BINDING SITE FOR RESIDUE IBM A 901
5
AC5
SOFTWARE
LEU A:693 , GLN A:699 , LEU A:701 , SER A:702 , LEU A:704 , TYR A:709
BINDING SITE FOR RESIDUE IBM A 902
6
AC6
SOFTWARE
ASP A:687 , LEU A:690 , ALA B:545 , ALA B:546 , VAL B:547 , HIS B:592
BINDING SITE FOR RESIDUE IBM A 903
7
AC7
SOFTWARE
HOH B:11 , HOH B:12 , HOH B:15 , HOH B:16 , ASP B:654 , GLU B:682 , THR B:723
BINDING SITE FOR RESIDUE MG B 900
8
AC8
SOFTWARE
LEU B:765 , VAL B:782 , PHE B:786 , GLN B:817 , PHE B:820
BINDING SITE FOR RESIDUE IBM B 901
9
AC9
SOFTWARE
GLN B:699 , LEU B:701 , SER B:702 , LEU B:704 , ILE B:706 , TYR B:709
BINDING SITE FOR RESIDUE IBM B 902
[
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SAPs(SNPs)/Variants
(2, 4)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_079310 (H653L, chain A/B, )
2: VAR_079311 (A831K, chain A/B, )
View:
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Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_079310
H
602
L
PDE6C_HUMAN
---
267606934
A/B
H
653
L
2
UniProt
VAR_079311
E
790
K
PDE6C_HUMAN
---
267606936
A/B
A
831
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PDEASE_I (A:653-664,B:653-664,A:653-664,B:65...)
;
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.
PDE6C_HUMAN
602-613
2
A:653-664
B:653-664
PDE5A_HUMAN
653-664
2
A:653-664
B:653-664
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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.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3jwrb_ (B:)
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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
:
automated matches
(21)
Human (Homo sapiens) [TaxId: 9606]
(21)
1a
d3jwrb_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3jwrB00 (B:532-859)
1b: CATH_3jwrA00 (A:537-859)
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Organisms
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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)
Homo sapiens. Organism_taxid: 9606.
(1)
1a
3jwrB00
B:532-859
1b
3jwrA00
A:537-859
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_PDEase_I_3jwrB01 (B:612-850)
1b: PFAM_PDEase_I_3jwrB02 (B:612-850)
2a: PFAM_PDE6_gamma_3jwrD01 (D:71-87)
2b: PFAM_PDE6_gamma_3jwrD02 (D:71-87)
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Clans
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Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-3jwrB01
B:612-850
1b
PDEase_I-3jwrB02
B:612-850
Clan
:
no clan defined [family: PDE6_gamma]
(2)
Family
:
PDE6_gamma
(2)
Homo sapiens (Human)
(1)
2a
PDE6_gamma-3jwrD01
D:71-87
2b
PDE6_gamma-3jwrD02
D:71-87
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Asym.Unit (122 KB)
Header - Asym.Unit
Biol.Unit 1 (60 KB)
Header - Biol.Unit 1
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