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Asym. Unit
Info
Asym.Unit (144 KB)
Biol.Unit 1 (72 KB)
Biol.Unit 2 (70 KB)
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(1)
Title
:
COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 2.1A.
Authors
:
M. Hohwy, L. Spadola, B. Lundquist, K. Von Wachenfeldt, S. Persdotter, P. Hawtin, J. Dahmen, I. Groth-Clausen, R. H. A. Folmer, K. Edman
Date
:
27 Sep 07 (Deposition) - 15 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Prostaglandin Biosynthesis, Fatty Acid Biosynthesis, Prostaglandin D2 Synthase, Pgds, Asthma, Cytoplasm, Isomerase, Lipid Synthesis
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Hohwy, L. Spadola, B. Lundquist, P. Hawtin, J. Dahmen, I. Groth-Clausen, E. Nilsson, S. Persdotter, K. Von Wachenfeldt, R. H. A. Folmer, K. Edman
Novel Prostaglandin D Synthase Inhibitors Generated By Fragment-Based Drug Design.
J. Med. Chem. V. 51 2178 2008
[
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Hetero Components
(3, 9)
Info
All Hetero Components
1a: PHENYL-5-(1H-PYRAZOL-3-YL)-1,3-THI... (D26a)
1b: PHENYL-5-(1H-PYRAZOL-3-YL)-1,3-THI... (D26b)
1c: PHENYL-5-(1H-PYRAZOL-3-YL)-1,3-THI... (D26c)
2a: GLUTATHIONE (GSHa)
2b: GLUTATHIONE (GSHb)
2c: GLUTATHIONE (GSHc)
2d: GLUTATHIONE (GSHd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
D26
3
Ligand/Ion
PHENYL-5-(1H-PYRAZOL-3-YL)-1,3-THIAZOLE
2
GSH
4
Ligand/Ion
GLUTATHIONE
3
MG
2
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:2032 , HOH A:2036 , HOH A:2037 , HOH B:2043 , HOH B:2044 , HOH B:2046
BINDING SITE FOR RESIDUE MG A1200
2
AC2
SOFTWARE
TYR A:8 , ARG A:14 , TRP A:39 , LYS A:43 , LYS A:50 , ILE A:51 , GLN A:63 , SER A:64 , HOH A:2004 , HOH A:2015 , HOH A:2035 , ASP B:97
BINDING SITE FOR RESIDUE GSH A1201
3
AC3
SOFTWARE
ASP A:97 , TYR B:8 , ARG B:14 , TRP B:39 , LYS B:43 , LYS B:50 , ILE B:51 , GLN B:63 , SER B:64 , D26 B:1201 , HOH B:2087 , HOH B:2088
BINDING SITE FOR RESIDUE GSH B1200
4
AC4
SOFTWARE
MET B:11 , GLY B:13 , ARG B:14 , MET B:99 , TRP B:104 , TYR B:152 , GSH B:1200 , HOH B:2085
BINDING SITE FOR RESIDUE D26 B1201
5
AC5
SOFTWARE
HOH C:2021 , HOH C:2026 , HOH C:2027 , HOH D:2022 , HOH D:2025 , HOH D:2028
BINDING SITE FOR RESIDUE MG C1200
6
AC6
SOFTWARE
TYR C:8 , ARG C:14 , TRP C:39 , LYS C:43 , LYS C:50 , ILE C:51 , GLN C:63 , SER C:64 , D26 C:1202 , HOH C:2014 , HOH C:2025 , HOH C:2029 , HOH C:2061 , ASP D:97
BINDING SITE FOR RESIDUE GSH C1201
7
AC7
SOFTWARE
MET C:11 , GLY C:13 , ARG C:14 , ASP C:96 , MET C:99 , TRP C:104 , TYR C:152 , GSH C:1201 , HOH C:2060
BINDING SITE FOR RESIDUE D26 C1202
8
AC8
SOFTWARE
ASP C:97 , TYR D:8 , ARG D:14 , TRP D:39 , LYS D:43 , LYS D:50 , ILE D:51 , PRO D:52 , GLN D:63 , SER D:64 , D26 D:1201 , HOH D:2005 , HOH D:2013 , HOH D:2026
BINDING SITE FOR RESIDUE GSH D1200
9
AC9
SOFTWARE
GLY D:13 , ARG D:14 , MET D:99 , TRP D:104 , TYR D:152 , GSH D:1200 , HOH D:2044
BINDING SITE FOR RESIDUE D26 D1201
[
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]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: GST_NTER (A:2-79,B:2-79,C:2-79,D:2-79)
2: GST_CTER (A:81-199,B:81-199,C:81-199,D:81-19...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
GST_NTER
PS50404
Soluble glutathione S-transferase N-terminal domain profile.
HPGDS_HUMAN
2-79
4
A:2-79
B:2-79
C:2-79
D:2-79
2
GST_CTER
PS50405
Soluble glutathione S-transferase C-terminal domain profile.
HPGDS_HUMAN
81-199
4
A:81-199
B:81-199
C:81-199
D:81-199
[
close PROSITE info
]
Exons
(5, 20)
Info
All Exons
Exon 1.2a (A:2-45 | B:2-45 | C:2-45 | D:2-45)
Exon 1.3 (A:45-76 | B:45-76 | C:45-76 | D:45...)
Exon 1.4 (A:76-112 | B:76-112 | C:76-105 | D...)
Exon 1.6 (A:113-145 | B:113-145 | C:115-145 ...)
Exon 1.7 (A:146-199 | B:146-199 | C:146-199 ...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1a/1.2a
2: Boundary 1.2a/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.6
5: Boundary 1.6/1.7
6: Boundary 1.7/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1a
ENST00000295256
1a
ENSE00001428701
chr4:
95264027-95263946
82
HPGDS_HUMAN
-
0
0
-
-
1.2a
ENST00000295256
2a
ENSE00002147371
chr4:
95255789-95255648
142
HPGDS_HUMAN
1-45
45
4
A:2-45
B:2-45
C:2-45
D:2-45
44
44
44
44
1.3
ENST00000295256
3
ENSE00001238639
chr4:
95239116-95239024
93
HPGDS_HUMAN
45-76
32
4
A:45-76
B:45-76
C:45-76
D:45-76
32
32
32
32
1.4
ENST00000295256
4
ENSE00001071670
chr4:
95229894-95229785
110
HPGDS_HUMAN
76-112
37
4
A:76-112
B:76-112
C:76-105
D:76-112
37
37
30
37
1.6
ENST00000295256
6
ENSE00001071668
chr4:
95223395-95223297
99
HPGDS_HUMAN
113-145
33
4
A:113-145
B:113-145
C:115-145
D:113-145
33
33
31
33
1.7
ENST00000295256
7
ENSE00001302624
chr4:
95220795-95219686
1110
HPGDS_HUMAN
146-199
54
4
A:146-199
B:146-199
C:146-199
D:146-199
54
54
54
54
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2vcxa1 (A:76-199)
1b: SCOP_d2vcxb1 (B:76-199)
1c: SCOP_d2vcxc1 (C:76-199)
1d: SCOP_d2vcxd1 (D:76-199)
2a: SCOP_d2vcxa2 (A:2-75)
2b: SCOP_d2vcxb2 (B:2-75)
2c: SCOP_d2vcxc2 (C:2-75)
2d: SCOP_d2vcxd2 (D:2-75)
View:
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Classes
(
)
(
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Folds
(
)
(
)
Superfamilies
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)
(
)
Families
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)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
GST C-terminal domain-like
(353)
Superfamily
:
GST C-terminal domain-like
(353)
Family
:
Glutathione S-transferase (GST), C-terminal domain
(263)
Protein domain
:
automated matches
(50)
Human (Homo sapiens) [TaxId: 9606]
(35)
1a
d2vcxa1
A:76-199
1b
d2vcxb1
B:76-199
1c
d2vcxc1
C:76-199
1d
d2vcxd1
D:76-199
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thioredoxin fold
(994)
Superfamily
:
Thioredoxin-like
(992)
Family
:
automated matches
(347)
Protein domain
:
automated matches
(347)
Human (Homo sapiens) [TaxId: 9606]
(87)
2a
d2vcxa2
A:2-75
2b
d2vcxb2
B:2-75
2c
d2vcxc2
C:2-75
2d
d2vcxd2
D:2-75
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2vcxA01 (A:2-75,A:184-199)
1b: CATH_2vcxB01 (B:2-75,B:184-199)
1c: CATH_2vcxC01 (C:2-75,C:184-199)
1d: CATH_2vcxD01 (D:2-75,D:184-199)
2a: CATH_2vcxA02 (A:76-183)
2b: CATH_2vcxB02 (B:76-183)
2c: CATH_2vcxD02 (D:76-183)
2d: CATH_2vcxC02 (C:76-183)
View:
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(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Glutaredoxin
(620)
Homologous Superfamily
:
Glutaredoxin
(617)
Human (Homo sapiens)
(186)
1a
2vcxA01
A:2-75,A:184-199
1b
2vcxB01
B:2-75,B:184-199
1c
2vcxC01
C:2-75,C:184-199
1d
2vcxD01
D:2-75,D:184-199
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
(267)
Homologous Superfamily
:
[code=1.20.1050.10, no name defined]
(249)
Human (Homo sapiens)
(119)
2a
2vcxA02
A:76-183
2b
2vcxB02
B:76-183
2c
2vcxD02
D:76-183
2d
2vcxC02
C:76-183
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_GST_C_2vcxD01 (D:81-185)
1b: PFAM_GST_C_2vcxD02 (D:81-185)
1c: PFAM_GST_C_2vcxD03 (D:81-185)
1d: PFAM_GST_C_2vcxD04 (D:81-185)
2a: PFAM_GST_N_2vcxD05 (D:4-73)
2b: PFAM_GST_N_2vcxD06 (D:4-73)
2c: PFAM_GST_N_2vcxD07 (D:4-73)
2d: PFAM_GST_N_2vcxD08 (D:4-73)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
GST_C
(118)
Family
:
GST_C
(102)
Homo sapiens (Human)
(47)
1a
GST_C-2vcxD01
D:81-185
1b
GST_C-2vcxD02
D:81-185
1c
GST_C-2vcxD03
D:81-185
1d
GST_C-2vcxD04
D:81-185
Clan
:
Thioredoxin
(367)
Family
:
GST_N
(88)
Homo sapiens (Human)
(45)
2a
GST_N-2vcxD05
D:4-73
2b
GST_N-2vcxD06
D:4-73
2c
GST_N-2vcxD07
D:4-73
2d
GST_N-2vcxD08
D:4-73
[
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Asym.Unit (144 KB)
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