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4OGB
Biol. Unit 1
Info
Asym.Unit (239 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (61 KB)
Biol.Unit 3 (61 KB)
Biol.Unit 4 (62 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE CATALYTIC DOMAIN OF PDE4D2 WITH COMPOUND 2
Authors
:
S. C. Feil, M. W. Parker
Date
:
15 Jan 14 (Deposition) - 21 Jan 15 (Release) - 21 Jan 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.03
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-Inhibitor Complex, Hydrolase-Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
B. L. Howard, J. L. Nankervis, S. C. Feil, D. T. Manallack, J. K. Holien, Z. Zhen, I. G. Jennings, B. M. Abbott, M. W. Parker, P. E. Thompson
The Pde Inhibition Profile Of Ly294002 And Tetrahydropyrany Analogues Reveals A Chromone Motif For The Development Of Pde Inhibitors
To Be Published
[
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]
Hetero Components
(4, 12)
Info
All Hetero Components
1a: (2R)-8-(3,4-DIMETHOXYPHENYL)-6-MET... (2SRa)
1b: (2R)-8-(3,4-DIMETHOXYPHENYL)-6-MET... (2SRb)
1c: (2R)-8-(3,4-DIMETHOXYPHENYL)-6-MET... (2SRc)
1d: (2R)-8-(3,4-DIMETHOXYPHENYL)-6-MET... (2SRd)
2a: DIMETHYL SULFOXIDE (DMSa)
2b: DIMETHYL SULFOXIDE (DMSb)
2c: DIMETHYL SULFOXIDE (DMSc)
2d: DIMETHYL SULFOXIDE (DMSd)
2e: DIMETHYL SULFOXIDE (DMSe)
2f: DIMETHYL SULFOXIDE (DMSf)
3a: 1,2-ETHANEDIOL (EDOa)
3aa: 1,2-ETHANEDIOL (EDOaa)
3ab: 1,2-ETHANEDIOL (EDOab)
3ac: 1,2-ETHANEDIOL (EDOac)
3ad: 1,2-ETHANEDIOL (EDOad)
3ae: 1,2-ETHANEDIOL (EDOae)
3af: 1,2-ETHANEDIOL (EDOaf)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
3p: 1,2-ETHANEDIOL (EDOp)
3q: 1,2-ETHANEDIOL (EDOq)
3r: 1,2-ETHANEDIOL (EDOr)
3s: 1,2-ETHANEDIOL (EDOs)
3t: 1,2-ETHANEDIOL (EDOt)
3u: 1,2-ETHANEDIOL (EDOu)
3v: 1,2-ETHANEDIOL (EDOv)
3w: 1,2-ETHANEDIOL (EDOw)
3x: 1,2-ETHANEDIOL (EDOx)
3y: 1,2-ETHANEDIOL (EDOy)
3z: 1,2-ETHANEDIOL (EDOz)
4a: 4-(2-HYDROXYETHYL)-1-PIPERAZINE ET... (EPEa)
5a: DI(HYDROXYETHYL)ETHER (PEGa)
5b: DI(HYDROXYETHYL)ETHER (PEGb)
5c: DI(HYDROXYETHYL)ETHER (PEGc)
5d: DI(HYDROXYETHYL)ETHER (PEGd)
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
2SR
1
Ligand/Ion
(2R)-8-(3,4-DIMETHOXYPHENYL)-6-METHYL-2-(TETRAHYDRO-2H-PYRAN-4-YL)-2H-CHROMEN-4-OL
2
DMS
2
Ligand/Ion
DIMETHYL SULFOXIDE
3
EDO
8
Ligand/Ion
1,2-ETHANEDIOL
4
EPE
-1
Ligand/Ion
4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID
5
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
6
ZN
-1
Ligand/Ion
ZINC ION
[
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]
Sites
(18, 18)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: CC2 (SOFTWARE)
16: EC7 (SOFTWARE)
17: FC8 (SOFTWARE)
18: FC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS A:160 , MET A:273 , LEU A:319 , MET A:357 , SER A:368 , GLN A:369 , PHE A:372 , ILE A:376
BINDING SITE FOR RESIDUE 2SR A 501
02
AC2
SOFTWARE
GLU A:218 , LYS C:239
BINDING SITE FOR RESIDUE EDO A 502
03
AC3
SOFTWARE
LEU A:132 , LYS A:136 , HOH A:628 , ASP D:394
BINDING SITE FOR RESIDUE EDO A 503
04
AC4
SOFTWARE
GLU A:150 , ASP A:151 , TYR A:153 , HOH A:640 , ARG C:346
BINDING SITE FOR RESIDUE PEG A 504
05
AC5
SOFTWARE
LYS A:255 , GLN A:256 , GLU D:182 , DMS D:504
BINDING SITE FOR RESIDUE EDO A 505
06
AC6
SOFTWARE
PHE A:238 , PHE A:249 , ARG A:257 , HOH A:609 , HOH A:631
BINDING SITE FOR RESIDUE EDO A 506
07
AC7
SOFTWARE
ASN A:278
BINDING SITE FOR RESIDUE EDO A 507
08
AC8
SOFTWARE
LYS A:239 , GLN A:242 , GLU A:243 , HOH A:608 , ASN C:216 , GLN D:242
BINDING SITE FOR RESIDUE EDO A 508
09
AC9
SOFTWARE
HIS A:164 , HIS A:200 , ASP A:201 , ASP A:318 , HOH A:668 , HOH A:707
BINDING SITE FOR RESIDUE ZN A 509
10
BC1
SOFTWARE
ASP A:201 , HOH A:606 , HOH A:614 , HOH A:616 , HOH A:668 , HOH A:708
BINDING SITE FOR RESIDUE ZN A 510
11
BC2
SOFTWARE
PRO A:138 , ASP A:140 , THR A:141 , HOH A:686
BINDING SITE FOR RESIDUE DMS A 511
12
BC3
SOFTWARE
LYS A:262 , ILE A:265 , ASP A:266 , HOH A:633 , HOH B:616
BINDING SITE FOR RESIDUE EDO A 512
13
BC4
SOFTWARE
HIS A:105 , VAL A:106 , PHE A:107 , ARG A:108 , GLN A:327 , GLN A:331
BINDING SITE FOR RESIDUE DMS A 513
14
BC5
SOFTWARE
HIS A:152 , GLU A:243 , SER C:217 , ARG C:350
BINDING SITE FOR RESIDUE EDO A 514
15
CC2
SOFTWARE
GLN A:258 , ASN B:214 , EDO B:507 , HOH B:625 , SER D:294 , SER D:295
BINDING SITE FOR RESIDUE EDO B 506
16
EC7
SOFTWARE
EDO A:505 , SER D:177 , GLU D:182
BINDING SITE FOR RESIDUE DMS D 504
17
FC8
SOFTWARE
THR A:134 , ASN A:251 , GLN A:256 , PRO D:179 , ASP D:391 , HOH D:717
BINDING SITE FOR RESIDUE EDO D 514
18
FC9
SOFTWARE
THR A:134 , HOH A:661 , ASP D:391 , EDO D:503 , PEG D:516 , HOH D:717
BINDING SITE FOR RESIDUE PEG D 515
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
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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.
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SCOP Domains
(0, 0)
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CATH Domains
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Pfam Domains
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Protein & NOT Variant
Protein & NOT Site
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Chain A
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (239 KB)
Header - Asym.Unit
Biol.Unit 1 (62 KB)
Header - Biol.Unit 1
Biol.Unit 2 (61 KB)
Header - Biol.Unit 2
Biol.Unit 3 (61 KB)
Header - Biol.Unit 3
Biol.Unit 4 (62 KB)
Header - Biol.Unit 4
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