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3SL3
Biol. Unit 3
Info
Asym.Unit (240 KB)
Biol.Unit 1 (63 KB)
Biol.Unit 2 (61 KB)
Biol.Unit 3 (62 KB)
Biol.Unit 4 (63 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE APO FORM OF THE CATALYTIC DOMAIN OF PDE4D2
Authors
:
S. F. Feil
Date
:
24 Jun 11 (Deposition) - 26 Oct 11 (Release) - 14 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
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 Mechanism, Camp Hydrolysis, Hydrolase
(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
[
close entry info
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Hetero Components
(4, 15)
Info
All Hetero Components
1a: DIMETHYL SULFOXIDE (DMSa)
1b: DIMETHYL SULFOXIDE (DMSb)
1c: DIMETHYL SULFOXIDE (DMSc)
1d: DIMETHYL SULFOXIDE (DMSd)
1e: DIMETHYL SULFOXIDE (DMSe)
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)
2ae: 1,2-ETHANEDIOL (EDOae)
2af: 1,2-ETHANEDIOL (EDOaf)
2ag: 1,2-ETHANEDIOL (EDOag)
2ah: 1,2-ETHANEDIOL (EDOah)
2ai: 1,2-ETHANEDIOL (EDOai)
2aj: 1,2-ETHANEDIOL (EDOaj)
2ak: 1,2-ETHANEDIOL (EDOak)
2al: 1,2-ETHANEDIOL (EDOal)
2am: 1,2-ETHANEDIOL (EDOam)
2an: 1,2-ETHANEDIOL (EDOan)
2ao: 1,2-ETHANEDIOL (EDOao)
2ap: 1,2-ETHANEDIOL (EDOap)
2aq: 1,2-ETHANEDIOL (EDOaq)
2ar: 1,2-ETHANEDIOL (EDOar)
2as: 1,2-ETHANEDIOL (EDOas)
2at: 1,2-ETHANEDIOL (EDOat)
2au: 1,2-ETHANEDIOL (EDOau)
2av: 1,2-ETHANEDIOL (EDOav)
2aw: 1,2-ETHANEDIOL (EDOaw)
2ax: 1,2-ETHANEDIOL (EDOax)
2ay: 1,2-ETHANEDIOL (EDOay)
2az: 1,2-ETHANEDIOL (EDOaz)
2b: 1,2-ETHANEDIOL (EDOb)
2ba: 1,2-ETHANEDIOL (EDOba)
2bb: 1,2-ETHANEDIOL (EDObb)
2bc: 1,2-ETHANEDIOL (EDObc)
2bd: 1,2-ETHANEDIOL (EDObd)
2be: 1,2-ETHANEDIOL (EDObe)
2bf: 1,2-ETHANEDIOL (EDObf)
2bg: 1,2-ETHANEDIOL (EDObg)
2bh: 1,2-ETHANEDIOL (EDObh)
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: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
4c: DI(HYDROXYETHYL)ETHER (PEGc)
4d: DI(HYDROXYETHYL)ETHER (PEGd)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
5c: PHOSPHATE ION (PO4c)
5d: PHOSPHATE ION (PO4d)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
6d: ZINC ION (ZNd)
6e: ZINC ION (ZNe)
6f: ZINC ION (ZNf)
6g: ZINC ION (ZNg)
6h: ZINC ION (ZNh)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
DMS
1
Ligand/Ion
DIMETHYL SULFOXIDE
2
EDO
12
Ligand/Ion
1,2-ETHANEDIOL
3
EPE
1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
PEG
-1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PO4
1
Ligand/Ion
PHOSPHATE ION
6
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(22, 22)
Info
All Sites
01: AC9 (SOFTWARE)
02: BC3 (SOFTWARE)
03: CC1 (SOFTWARE)
04: CC3 (SOFTWARE)
05: EC3 (SOFTWARE)
06: EC4 (SOFTWARE)
07: EC5 (SOFTWARE)
08: EC6 (SOFTWARE)
09: EC7 (SOFTWARE)
10: EC8 (SOFTWARE)
11: EC9 (SOFTWARE)
12: FC1 (SOFTWARE)
13: FC2 (SOFTWARE)
14: FC3 (SOFTWARE)
15: FC4 (SOFTWARE)
16: FC5 (SOFTWARE)
17: FC6 (SOFTWARE)
18: FC7 (SOFTWARE)
19: FC8 (SOFTWARE)
20: FC9 (SOFTWARE)
21: GC1 (SOFTWARE)
22: HC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC9
SOFTWARE
EDO A:3 , ASP A:151 , TYR A:153 , HIS A:154 , ALA A:155 , HOH A:545 , ASP C:156 , HOH C:483
BINDING SITE FOR RESIDUE EDO A 9
02
BC3
SOFTWARE
EDO A:5 , HIS A:154 , ASP A:156 , VAL A:157 , PRO A:205 , HOH C:474
BINDING SITE FOR RESIDUE EDO A 12
03
CC1
SOFTWARE
THR A:148 , HIS A:152 , GLU A:243 , HOH A:555 , SER C:217 , ARG C:350
BINDING SITE FOR RESIDUE EDO A 19
04
CC3
SOFTWARE
LYS A:239 , GLN A:242 , GLU A:243 , EDO C:18 , ASN C:216 , SER C:217 , GLU C:218 , GLN D:242
BINDING SITE FOR RESIDUE EDO A 21
05
EC3
SOFTWARE
ARG A:350 , HIS C:152 , GLU C:243
BINDING SITE FOR RESIDUE EDO C 1
06
EC4
SOFTWARE
GLU A:244 , ASN C:214 , ARG C:350 , MET C:352 , HOH C:506 , LYS D:254
BINDING SITE FOR RESIDUE EDO C 7
07
EC5
SOFTWARE
GLU A:218 , TYR C:223 , HIS C:232 , ALA C:235 , HOH C:463
BINDING SITE FOR RESIDUE EDO C 2
08
EC6
SOFTWARE
ASP A:156 , EDO C:13 , GLU C:150 , ASP C:151 , TYR C:153 , ASN C:162
BINDING SITE FOR RESIDUE EDO C 3
09
EC7
SOFTWARE
HIS C:105 , VAL C:106 , PHE C:107 , ARG C:108 , GLU C:111 , GLN C:327 , LEU C:328 , GLN C:331
BINDING SITE FOR RESIDUE EPE C 4
10
EC8
SOFTWARE
ARG C:257 , ARG C:261
BINDING SITE FOR RESIDUE DMS C 5
11
EC9
SOFTWARE
LYS C:262 , ASP C:266 , ASN D:224
BINDING SITE FOR RESIDUE EDO C 6
12
FC1
SOFTWARE
LYS C:275 , HOH C:465
BINDING SITE FOR RESIDUE EDO C 12
13
FC2
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 8
14
FC3
SOFTWARE
ASP C:203 , LEU C:219
BINDING SITE FOR RESIDUE EDO C 9
15
FC4
SOFTWARE
ASP C:156 , VAL C:157 , PRO C:205 , ARG C:342 , ARG C:346 , HOH C:468 , HOH C:502
BINDING SITE FOR RESIDUE EDO C 10
16
FC5
SOFTWARE
HIS C:160 , HIS C:204 , GLY C:206 , VAL C:207 , GLU C:339 , PHE C:340 , GLN C:343
BINDING SITE FOR RESIDUE EDO C 11
17
FC6
SOFTWARE
EDO C:3 , ASN C:115 , ALA C:155 , ASN C:161 , ASN C:162 , ILE C:163
BINDING SITE FOR RESIDUE EDO C 13
18
FC7
SOFTWARE
PO4 C:16 , ASP C:201 , HOH C:456 , HOH C:457 , HOH C:458 , HOH C:459
BINDING SITE FOR RESIDUE ZN C 14
19
FC8
SOFTWARE
PO4 C:16 , HIS C:164 , HIS C:200 , ASP C:201 , ASP C:318 , HOH C:458
BINDING SITE FOR RESIDUE ZN C 15
20
FC9
SOFTWARE
ZN C:14 , ZN C:15 , HOH C:58 , HIS C:160 , HIS C:164 , ASP C:201 , ASP C:318 , HOH C:458
BINDING SITE FOR RESIDUE PO4 C 16
21
GC1
SOFTWARE
EDO A:21 , GLU A:243 , HOH A:555 , GLU C:218
BINDING SITE FOR RESIDUE EDO C 18
22
HC3
SOFTWARE
ASP C:225 , HOH C:461 , GLN D:258 , LYS D:262 , ASP D:266
BINDING SITE FOR RESIDUE PEG D 8
[
close Site info
]
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)
[
close SNP/Variant info
]
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
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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_d3sl3a_ (A:)
1b: SCOP_d3sl3b_ (B:)
1c: SCOP_d3sl3c_ (C:)
1d: SCOP_d3sl3d_ (D:)
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
d3sl3a_
A:
1b
d3sl3b_
B:
1c
d3sl3c_
C:
1d
d3sl3d_
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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Label:
Sorry, no Info available
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Chain C
Asymmetric Unit 1
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