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3JWQ
Biol. Unit 1
Info
Asym.Unit (223 KB)
Biol.Unit 1 (57 KB)
Biol.Unit 2 (57 KB)
Biol.Unit 3 (57 KB)
Biol.Unit 4 (56 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF CHIMERIC PDE5/PDE6 CATALYTIC DOMAIN COMPLEXED WITH SILDENAFIL
Authors
:
B. Barren, L. Gakhar, H. Muradov, K. K. Boyd, S. Ramaswamy, N. O. Artemye
Date
:
18 Sep 09 (Deposition) - 13 Oct 09 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.87
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
:
Mostly Alpha, Allosteric Enzyme, Cgmp, Cgmp-Binding, Hydrolase, Magnesium, Metal-Binding, Nucleotide-Binding, Phosphoprotein, Cell Membrane, Lipoprotein, Membrane, Methylation, Prenylation, Sensory Transduction, Vision
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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)
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
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-... (VIAa)
2b: 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-... (VIAb)
2c: 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-... (VIAc)
2d: 5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-... (VIAd)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
MG
-1
Ligand/Ion
MAGNESIUM ION
2
VIA
1
Ligand/Ion
5-{2-ETHOXY-5-[(4-METHYLPIPERAZIN-1-YL)SULFONYL]PHENYL}-1-METHYL-3-PROPYL-1H,6H,7H-PYRAZOLO[4,3-D]PYRIMIDIN-7-ONE
3
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: BC3 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:6 , HIS A:617 , HIS A:653 , ASP A:654 , ASP A:764 , MG A:900
BINDING SITE FOR RESIDUE ZN A 899
2
AC2
SOFTWARE
HOH A:4 , HOH A:6 , HOH A:7 , HOH A:8 , ASP A:654 , THR A:723 , ZN A:899
BINDING SITE FOR RESIDUE MG A 900
3
AC3
SOFTWARE
TYR A:612 , MET A:804 , GLN A:817 , PHE A:820
BINDING SITE FOR RESIDUE VIA A 901
4
BC3
SOFTWARE
ARG A:794 , TYR D:612 , MET D:804 , GLN D:817 , PHE D:820
BINDING SITE FOR RESIDUE VIA D 901
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_079310 (H653L, chain A, )
2: VAR_079311 (A831K, chain A, )
View:
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_079310
H
602
L
PDE6C_HUMAN
---
267606934
A
H
653
L
2
UniProt
VAR_079311
E
790
K
PDE6C_HUMAN
---
267606936
A
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)
;
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
1
A:653-664
-
-
-
PDE5A_HUMAN
653-664
1
A:653-664
-
-
-
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Exons
(0, 0)
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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_d3jwqa_ (A:)
1b: SCOP_d3jwqb_ (B:)
1c: SCOP_d3jwqc_ (C:)
1d: SCOP_d3jwqd_ (D:)
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Protein Domains
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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
:
automated matches
(21)
Human (Homo sapiens) [TaxId: 9606]
(21)
1a
d3jwqa_
A:
1b
d3jwqb_
B:
1c
d3jwqc_
C:
1d
d3jwqd_
D:
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3jwqC00 (C:533-859)
1b: CATH_3jwqA00 (A:536-859)
1c: CATH_3jwqB00 (B:536-859)
1d: CATH_3jwqD00 (D:537-859)
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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
3jwqC00
C:533-859
1b
3jwqA00
A:536-859
1c
3jwqB00
B:536-859
1d
3jwqD00
D:537-859
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_PDEase_I_3jwqD01 (D:612-850)
1b: PFAM_PDEase_I_3jwqD02 (D:612-850)
1c: PFAM_PDEase_I_3jwqD03 (D:612-850)
1d: PFAM_PDEase_I_3jwqD04 (D:612-850)
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Clan
:
HD_PDEase
(93)
Family
:
PDEase_I
(77)
Homo sapiens (Human)
(71)
1a
PDEase_I-3jwqD01
D:612-850
1b
PDEase_I-3jwqD02
D:612-850
1c
PDEase_I-3jwqD03
D:612-850
1d
PDEase_I-3jwqD04
D:612-850
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (223 KB)
Header - Asym.Unit
Biol.Unit 1 (57 KB)
Header - Biol.Unit 1
Biol.Unit 2 (57 KB)
Header - Biol.Unit 2
Biol.Unit 3 (57 KB)
Header - Biol.Unit 3
Biol.Unit 4 (56 KB)
Header - Biol.Unit 4
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