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2VD0
Asym. Unit
Info
Asym.Unit (144 KB)
Biol.Unit 1 (73 KB)
Biol.Unit 2 (70 KB)
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(1)
Title
:
COMPLEX STRUCTURE OF PROSTAGLANDIN D2 SYNTHASE AT 2.2A.
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
:
28 Sep 07 (Deposition) - 15 Apr 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
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, 5)
Info
All Hetero Components
1a: 2-{[(2E)-3-(3,4-DIMETHOXYPHENYL)PR... (D27a)
2a: GLYCEROL (GOLa)
3a: GLUTATHIONE (GSHa)
3b: GLUTATHIONE (GSHb)
3c: GLUTATHIONE (GSHc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
D27
1
Ligand/Ion
2-{[(2E)-3-(3,4-DIMETHOXYPHENYL)PROP-2-ENOYL]AMINO}BENZOIC ACID
2
GOL
1
Ligand/Ion
GLYCEROL
3
GSH
3
Ligand/Ion
GLUTATHIONE
[
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]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
MET B:11 , GLY B:13 , ARG B:14 , MET B:99 , TRP B:104 , TYR B:152 , CYS B:156 , LEU B:199
BINDING SITE FOR RESIDUE D27 B1200
2
AC2
SOFTWARE
TYR A:8 , ARG A:14 , TRP A:39 , LYS A:43 , GLY A:49 , LYS A:50 , ILE A:51 , GLN A:63 , SER A:64 , HOH A:2089 , ASP B:97
BINDING SITE FOR RESIDUE GSH A1200
3
AC3
SOFTWARE
ASP A:97 , TYR B:8 , ARG B:14 , TRP B:39 , LYS B:43 , LYS B:50 , ILE B:51 , PRO B:52 , GLN B:63 , SER B:64 , HOH B:2005 , HOH B:2087
BINDING SITE FOR RESIDUE GSH B1201
4
AC4
SOFTWARE
ASP C:97 , TYR D:8 , ARG D:14 , TRP D:39 , LYS D:43 , GLY D:49 , LYS D:50 , ILE D:51 , GLN D:63 , SER D:64
BINDING SITE FOR RESIDUE GSH D1200
5
AC5
SOFTWARE
LYS A:108 , ASN A:170 , ARG C:194 , THR C:197 , HOH C:2075 , HOH C:2076
BINDING SITE FOR RESIDUE GOL C1200
[
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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:
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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
[
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]
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:76-112 | D...)
Exon 1.6 (A:113-145 | B:113-145 | C:113-145 ...)
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:76-112
D:76-112
37
37
37
37
1.6
ENST00000295256
6
ENSE00001071668
chr4:
95223395-95223297
99
HPGDS_HUMAN
113-145
33
4
A:113-145
B:113-145
C:113-145
D:113-145
33
33
33
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
[
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]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2vd0a1 (A:76-199)
1b: SCOP_d2vd0b1 (B:76-199)
1c: SCOP_d2vd0c1 (C:76-199)
1d: SCOP_d2vd0d1 (D:76-199)
2a: SCOP_d2vd0a2 (A:2-75)
2b: SCOP_d2vd0b2 (B:2-75)
2c: SCOP_d2vd0c2 (C:2-75)
2d: SCOP_d2vd0d2 (D:2-75)
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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
d2vd0a1
A:76-199
1b
d2vd0b1
B:76-199
1c
d2vd0c1
C:76-199
1d
d2vd0d1
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
d2vd0a2
A:2-75
2b
d2vd0b2
B:2-75
2c
d2vd0c2
C:2-75
2d
d2vd0d2
D:2-75
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2vd0A01 (A:2-75,A:184-199)
1b: CATH_2vd0B01 (B:2-75,B:184-199)
1c: CATH_2vd0C01 (C:2-75,C:184-199)
1d: CATH_2vd0D01 (D:2-75,D:184-199)
2a: CATH_2vd0A02 (A:76-183)
2b: CATH_2vd0B02 (B:76-183)
2c: CATH_2vd0C02 (C:76-183)
2d: CATH_2vd0D02 (D:76-183)
View:
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Homologous Superfamilies
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)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Glutaredoxin
(620)
Homologous Superfamily
:
Glutaredoxin
(617)
Human (Homo sapiens)
(186)
1a
2vd0A01
A:2-75,A:184-199
1b
2vd0B01
B:2-75,B:184-199
1c
2vd0C01
C:2-75,C:184-199
1d
2vd0D01
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
2vd0A02
A:76-183
2b
2vd0B02
B:76-183
2c
2vd0C02
C:76-183
2d
2vd0D02
D:76-183
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_GST_C_2vd0D01 (D:81-185)
1b: PFAM_GST_C_2vd0D02 (D:81-185)
1c: PFAM_GST_C_2vd0D03 (D:81-185)
1d: PFAM_GST_C_2vd0D04 (D:81-185)
2a: PFAM_GST_N_2vd0D05 (D:4-73)
2b: PFAM_GST_N_2vd0D06 (D:4-73)
2c: PFAM_GST_N_2vd0D07 (D:4-73)
2d: PFAM_GST_N_2vd0D08 (D:4-73)
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(
)
(
)
Clan
:
GST_C
(118)
Family
:
GST_C
(102)
Homo sapiens (Human)
(47)
1a
GST_C-2vd0D01
D:81-185
1b
GST_C-2vd0D02
D:81-185
1c
GST_C-2vd0D03
D:81-185
1d
GST_C-2vd0D04
D:81-185
Clan
:
Thioredoxin
(367)
Family
:
GST_N
(88)
Homo sapiens (Human)
(45)
2a
GST_N-2vd0D05
D:4-73
2b
GST_N-2vd0D06
D:4-73
2c
GST_N-2vd0D07
D:4-73
2d
GST_N-2vd0D08
D:4-73
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Asym.Unit (144 KB)
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