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3SL3
Biol. Unit 4
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, 25)
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
2
Ligand/Ion
DIMETHYL SULFOXIDE
2
EDO
20
Ligand/Ion
1,2-ETHANEDIOL
3
EPE
-1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
4
PEG
2
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
PO4
1
Ligand/Ion
PHOSPHATE ION
6
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(36, 36)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC6 (SOFTWARE)
03: AC7 (SOFTWARE)
04: AC8 (SOFTWARE)
05: CC3 (SOFTWARE)
06: DC5 (SOFTWARE)
07: EC2 (SOFTWARE)
08: EC4 (SOFTWARE)
09: EC9 (SOFTWARE)
10: GC2 (SOFTWARE)
11: GC3 (SOFTWARE)
12: GC4 (SOFTWARE)
13: GC5 (SOFTWARE)
14: GC6 (SOFTWARE)
15: GC7 (SOFTWARE)
16: GC8 (SOFTWARE)
17: GC9 (SOFTWARE)
18: HC1 (SOFTWARE)
19: HC2 (SOFTWARE)
20: HC3 (SOFTWARE)
21: HC4 (SOFTWARE)
22: HC5 (SOFTWARE)
23: HC6 (SOFTWARE)
24: HC7 (SOFTWARE)
25: HC8 (SOFTWARE)
26: HC9 (SOFTWARE)
27: IC1 (SOFTWARE)
28: IC2 (SOFTWARE)
29: IC3 (SOFTWARE)
30: IC4 (SOFTWARE)
31: IC5 (SOFTWARE)
32: IC6 (SOFTWARE)
33: IC7 (SOFTWARE)
34: IC8 (SOFTWARE)
35: IC9 (SOFTWARE)
36: JC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC2
SOFTWARE
EDO A:20 , LEU A:188 , LYS A:255 , GLN A:256 , DMS D:6 , GLU D:182
BINDING SITE FOR RESIDUE EDO A 2
02
AC6
SOFTWARE
EDO A:7 , PHE A:135 , GLN A:256 , HOH A:511 , DMS D:6
BINDING SITE FOR RESIDUE EDO A 6
03
AC7
SOFTWARE
EDO A:6 , THR A:134 , LYS A:136 , EDO D:9 , PRO D:179 , ASP D:391
BINDING SITE FOR RESIDUE EDO A 7
04
AC8
SOFTWARE
GLN A:250 , ASN A:251 , HOH A:548 , HOH A:577 , HOH D:556
BINDING SITE FOR RESIDUE EDO A 8
05
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
06
DC5
SOFTWARE
GLU B:218 , HIS D:152 , LYS D:239 , HOH D:594
BINDING SITE FOR RESIDUE EDO B 11
07
EC2
SOFTWARE
HIS B:152 , GLU B:243 , HOH B:519 , THR D:215 , SER D:217 , GLU D:218 , LEU D:219 , ARG D:350
BINDING SITE FOR RESIDUE PEG B 17
08
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
09
EC9
SOFTWARE
LYS C:262 , ASP C:266 , ASN D:224
BINDING SITE FOR RESIDUE EDO C 6
10
GC2
SOFTWARE
ASP D:266 , GLN D:311
BINDING SITE FOR RESIDUE EDO D 4
11
GC3
SOFTWARE
EDO A:2 , EDO A:6 , SER D:177 , PRO D:179 , GLU D:182 , HOH D:553
BINDING SITE FOR RESIDUE DMS D 6
12
GC4
SOFTWARE
SER B:217 , HOH B:502 , EDO D:23 , THR D:148 , HIS D:152 , GLU D:243
BINDING SITE FOR RESIDUE EDO D 1
13
GC5
SOFTWARE
EDO A:7 , THR A:134 , PHE A:135 , ASN A:251 , GLN A:256 , PRO D:179 , ASP D:391
BINDING SITE FOR RESIDUE EDO D 9
14
GC6
SOFTWARE
EDO D:5 , LEU D:175 , THR D:178 , VAL D:388 , ASP D:391 , HOH D:541
BINDING SITE FOR RESIDUE EDO D 2
15
GC7
SOFTWARE
LEU D:181 , ALA D:183 , VAL D:184 , PHE D:185 , HOH D:553
BINDING SITE FOR RESIDUE EDO D 3
16
GC8
SOFTWARE
GLU D:150 , ASP D:151 , TYR D:153 , ASN D:162
BINDING SITE FOR RESIDUE DMS D 25
17
GC9
SOFTWARE
EDO D:2 , ASN D:100 , LYS D:101 , TRP D:102 , HOH D:550
BINDING SITE FOR RESIDUE EDO D 5
18
HC1
SOFTWARE
ASN D:100 , GLU D:128 , HIS D:173 , SER D:177
BINDING SITE FOR RESIDUE EDO D 27
19
HC2
SOFTWARE
HIS D:123
BINDING SITE FOR RESIDUE EDO D 7
20
HC3
SOFTWARE
ASP C:225 , HOH C:461 , GLN D:258 , LYS D:262 , ASP D:266
BINDING SITE FOR RESIDUE PEG D 8
21
HC4
SOFTWARE
ASN D:302 , TYR D:303 , SER D:304
BINDING SITE FOR RESIDUE EDO D 10
22
HC5
SOFTWARE
THR D:186 , LEU D:188 , GLU D:189 , SER D:259 , MET D:263 , HOH D:523
BINDING SITE FOR RESIDUE PEG D 11
23
HC6
SOFTWARE
ASP D:247 , PHE D:249 , ARG D:257
BINDING SITE FOR RESIDUE EDO D 12
24
HC7
SOFTWARE
ASP D:156 , VAL D:157 , ALA D:158 , GLU D:338 , GLU D:339 , HOH D:605
BINDING SITE FOR RESIDUE EDO D 13
25
HC8
SOFTWARE
PRO D:325 , LEU D:326 , GLN D:327 , HOH D:582
BINDING SITE FOR RESIDUE EDO D 14
26
HC9
SOFTWARE
GLU D:244 , ASN D:245 , SER D:294 , GLY D:296 , HOH D:520
BINDING SITE FOR RESIDUE EDO D 15
27
IC1
SOFTWARE
THR D:134 , LYS D:136 , ASN D:251 , GLN D:256
BINDING SITE FOR RESIDUE EDO D 16
28
IC2
SOFTWARE
PO4 D:19 , ASP D:201 , HOH D:535 , HOH D:536 , HOH D:537
BINDING SITE FOR RESIDUE ZN D 17
29
IC3
SOFTWARE
PO4 D:19 , HIS D:164 , HIS D:200 , ASP D:201 , ASP D:318
BINDING SITE FOR RESIDUE ZN D 18
30
IC4
SOFTWARE
ZN D:17 , ZN D:18 , HIS D:160 , HIS D:164 , ASP D:201 , ASP D:318 , HOH D:574
BINDING SITE FOR RESIDUE PO4 D 19
31
IC5
SOFTWARE
MET D:286 , THR D:289 , ASP D:305
BINDING SITE FOR RESIDUE EDO D 20
32
IC6
SOFTWARE
GLN D:127 , HOH D:507
BINDING SITE FOR RESIDUE EDO D 21
33
IC7
SOFTWARE
ASP D:98 , LYS D:101 , TRP D:102
BINDING SITE FOR RESIDUE EDO D 22
34
IC8
SOFTWARE
THR B:215 , ARG B:350 , EDO D:1 , THR D:148 , GLU D:243 , GLU D:244 , CYS D:246 , HOH D:554
BINDING SITE FOR RESIDUE EDO D 23
35
IC9
SOFTWARE
ASN D:321 , THR D:333 , ILE D:336 , GLN D:369 , HOH D:529
BINDING SITE FOR RESIDUE EDO D 24
36
JC1
SOFTWARE
ASP D:266 , GLN D:311
BINDING SITE FOR RESIDUE EDO D 26
[
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 D, )
2: VAR_069453 (E288A, chain D, )
3: VAR_069454 (G371D, chain D, )
4: VAR_069455 (I376T, 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
285
P
2
UniProt
VAR_069453
E
590
A
PDE4D_HUMAN
Disease (ACRDYS2)
---
D
E
288
A
3
UniProt
VAR_069454
G
673
D
PDE4D_HUMAN
Disease (ACRDYS2)
---
D
G
371
D
4
UniProt
VAR_069455
I
678
T
PDE4D_HUMAN
Disease (ACRDYS2)
---
D
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 (D: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
-
-
-
D:200-211
[
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]
Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d3sl3a_ (A:)
1b: SCOP_d3sl3b_ (B:)
1c: SCOP_d3sl3c_ (C:)
1d: SCOP_d3sl3d_ (D:)
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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
:
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 D
Asymmetric Unit 1
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