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3SL6
Biol. Unit 3
Info
Asym.Unit (232 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (59 KB)
Biol.Unit 3 (60 KB)
Biol.Unit 4 (60 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PDE4D2 WITH COMPOUND 12C
Authors
:
S. F. Feil
Date
:
24 Jun 11 (Deposition) - 26 Oct 11 (Release) - 14 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.44
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
:
Catalytic Domain, Camp Hydrolysis, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. L. Nankervis, S. C. Feil, N. C. Hancock, Z. Zheng, H. L. Ng, C. J. Morton, J. K. Holien, P. W. Ho, M. M. Frazzetto, I. G. Jennings, D. T. Manallack, T. J. Martin, P. E. Thompson, M. W. Parker
Thiophene Inhibitors Of Pde4: Crystal Structures Show A Second Binding Mode At The Catalytic Domain Of Pde4D2.
Bioorg. Med. Chem. Lett. V. 21 7089 2011
[
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
2a: 1,2-ETHANEDIOL (EDOa)
2aa: 1,2-ETHANEDIOL (EDOaa)
2ab: 1,2-ETHANEDIOL (EDOab)
2ac: 1,2-ETHANEDIOL (EDOac)
2ad: 1,2-ETHANEDIOL (EDOad)
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)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
4a: CYCLOPENTYL 6-(ETHYLCARBAMOYL)-2-[... (JN8a)
4b: CYCLOPENTYL 6-(ETHYLCARBAMOYL)-2-[... (JN8b)
4c: CYCLOPENTYL 6-(ETHYLCARBAMOYL)-2-[... (JN8c)
4d: CYCLOPENTYL 6-(ETHYLCARBAMOYL)-2-[... (JN8d)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
5e: ZINC ION (ZNe)
5f: ZINC ION (ZNf)
5g: ZINC ION (ZNg)
5h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMS
-1
Ligand/Ion
DIMETHYL SULFOXIDE
2
EDO
7
Ligand/Ion
1,2-ETHANEDIOL
3
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
JN8
1
Ligand/Ion
CYCLOPENTYL 6-(ETHYLCARBAMOYL)-2-[(THIOPHEN-2-YLACETYL)AMINO]-4,5,6,7-TETRAHYDROTHIENO[2,3-C]PYRIDINE-3-CARBOXYLATE
5
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(15, 15)
Info
All Sites
01: AC3 (SOFTWARE)
02: BC3 (SOFTWARE)
03: CC2 (SOFTWARE)
04: CC3 (SOFTWARE)
05: CC4 (SOFTWARE)
06: CC5 (SOFTWARE)
07: CC6 (SOFTWARE)
08: CC7 (SOFTWARE)
09: CC8 (SOFTWARE)
10: CC9 (SOFTWARE)
11: DC1 (SOFTWARE)
12: DC2 (SOFTWARE)
13: DC3 (SOFTWARE)
14: EC2 (SOFTWARE)
15: EC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC3
SOFTWARE
GLU A:218 , LYS C:239
BINDING SITE FOR RESIDUE EDO A 2
02
BC3
SOFTWARE
HIS A:152 , GLU A:243 , ARG C:350
BINDING SITE FOR RESIDUE EDO A 442
03
CC2
SOFTWARE
ARG A:350 , HIS C:152 , GLU C:243
BINDING SITE FOR RESIDUE EDO C 3
04
CC3
SOFTWARE
ZN C:11 , ASP C:201 , HOH C:462 , HOH C:464
BINDING SITE FOR RESIDUE ZN C 10
05
CC4
SOFTWARE
ZN C:10 , HIS C:164 , HIS C:200 , ASP C:201 , ASP C:318 , HOH C:467
BINDING SITE FOR RESIDUE ZN C 11
06
CC5
SOFTWARE
HIS C:105 , PHE C:107 , ARG C:108 , GLU C:111 , GLN C:327 , LEU C:328 , GLN C:331
BINDING SITE FOR RESIDUE EPE C 2
07
CC6
SOFTWARE
LEU C:175 , THR C:178 , TRP C:384 , ASP C:391 , ALA C:392
BINDING SITE FOR RESIDUE EDO C 440
08
CC7
SOFTWARE
HIS B:389 , PRO B:390 , THR C:134 , PHE C:135 , LYS C:136 , ASN C:251 , GLN C:256
BINDING SITE FOR RESIDUE EDO C 4
09
CC8
SOFTWARE
GLU C:150 , ASP C:151 , TYR C:153 , ALA C:155
BINDING SITE FOR RESIDUE EDO C 5
10
CC9
SOFTWARE
LYS B:290 , GLY B:296 , THR C:253 , LYS C:254 , LYS C:255
BINDING SITE FOR RESIDUE EDO C 7
11
DC1
SOFTWARE
LEU C:234 , PHE C:238 , ARG C:261 , LEU D:221 , ASN D:224
BINDING SITE FOR RESIDUE EDO C 8
12
DC2
SOFTWARE
LYS C:262 , ASP C:266 , ASN D:224 , ASP D:225
BINDING SITE FOR RESIDUE EDO C 9
13
DC3
SOFTWARE
TYR C:159 , LEU C:319 , ASN C:321 , THR C:333 , ILE C:336 , PHE C:340 , CYS C:358 , GLN C:369 , PHE C:372 , HOH C:463
BINDING SITE FOR RESIDUE JN8 C 441
14
EC2
SOFTWARE
ASN C:224 , SER C:226 , EDO D:9 , LYS D:262 , ILE D:265 , ASP D:266
BINDING SITE FOR RESIDUE EDO D 6
15
EC5
SOFTWARE
HOH C:14 , HOH C:42 , ASP C:225 , EDO D:6 , GLN D:258 , ARG D:261 , LYS D:262
BINDING SITE FOR RESIDUE EDO D 9
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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 (T285P, chain C, )
2: VAR_069453 (E288A, chain C, )
3: VAR_069454 (G371D, chain C, )
4: VAR_069455 (I376T, chain C, )
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)
---
C
T
285
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
C
E
288
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
C
G
371
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
C
I
376
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 (C: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
1
-
-
C:200-211
-
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
View:
Label:
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_d3sl6a_ (A:)
1b: SCOP_d3sl6b_ (B:)
1c: SCOP_d3sl6c_ (C:)
1d: SCOP_d3sl6d_ (D:)
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)
Protein Domains
(
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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
d3sl6a_
A:
1b
d3sl6b_
B:
1c
d3sl6c_
C:
1d
d3sl6d_
D:
[
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CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain C
Asymmetric Unit 1
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Asym.Unit (232 KB)
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