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1PD2
Asym. Unit
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Asym.Unit (91 KB)
Biol.Unit 1 (87 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE COMPLEX WITH GLUTATHIONE
Authors
:
M. Miyano, H. Ago
Date
:
14 Dec 98 (Deposition) - 13 Oct 99 (Release) - 14 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : 1,2
Biol. Unit 1: 1,2 (1x)
Keywords
:
Hematopoietic Prostaglandin D Synthase, Pgds, Gst, Sigma-Class Gst, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Kanaoka, H. Ago, E. Inagaki, T. Nanayama, M. Miyano, R. Kikuno, Y. Fujii, N. Eguchi, H. Toh, Y. Urade, O. Hayaishi
Cloning And Crystal Structure Of Hematopoietic Prostaglandi D Synthase.
Cell(Cambridge, Mass. ) V. 90 1085 1997
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: GLUTATHIONE (GSHa)
1b: GLUTATHIONE (GSHb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GSH
2
Ligand/Ion
GLUTATHIONE
[
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]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR 1:8 , ARG 1:14 , TRP 1:39 , LYS 1:43 , LYS 1:50 , ILE 1:51 , GLN 1:63 , SER 1:64 , HOH 1:320 , ASP 2:97
BINDING SITE FOR RESIDUE GSH 1 301
2
AC2
SOFTWARE
ASP 1:97 , TYR 2:8 , ARG 2:14 , TRP 2:39 , LYS 2:43 , LYS 2:50 , ILE 2:51 , GLN 2:63 , SER 2:64 , HOH 2:311 , HOH 2:323
BINDING SITE FOR RESIDUE GSH 2 302
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: GST_NTER (1:2-79,2:2-79)
2: GST_CTER (1:81-199,2:81-199)
;
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_RAT
2-79
2
1:2-79
2:2-79
2
GST_CTER
PS50405
Soluble glutathione S-transferase C-terminal domain profile.
HPGDS_RAT
81-199
2
1:81-199
2:81-199
[
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]
Exons
(5, 10)
Info
All Exons
Exon 1.2 (1:1-45 | 2:1-45)
Exon 1.3 (1:45-76 | 2:45-76)
Exon 1.4 (1:76-112 | 2:76-112)
Exon 1.5 (1:113-145 | 2:113-145)
Exon 1.6 (1:146-199 | 2:146-199)
View:
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All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/1.5
5: Boundary 1.5/1.6
6: Boundary 1.6/-
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
1.1
ENSRNOT00000008826
1
ENSRNOE00000060741
chr4:
94636147-94635796
352
HPGDS_RAT
-
0
0
-
-
1.2
ENSRNOT00000008826
2
ENSRNOE00000060859
chr4:
94629309-94629168
142
HPGDS_RAT
1-45
45
2
1:1-45
2:1-45
45
45
1.3
ENSRNOT00000008826
3
ENSRNOE00000061100
chr4:
94626200-94626108
93
HPGDS_RAT
45-76
32
2
1:45-76
2:45-76
32
32
1.4
ENSRNOT00000008826
4
ENSRNOE00000061216
chr4:
94622786-94622677
110
HPGDS_RAT
76-112
37
2
1:76-112
2:76-112
37
37
1.5
ENSRNOT00000008826
5
ENSRNOE00000061376
chr4:
94615216-94615118
99
HPGDS_RAT
113-145
33
2
1:113-145
2:113-145
33
33
1.6
ENSRNOT00000008826
6
ENSRNOE00000061562
chr4:
94611985-94611611
375
HPGDS_RAT
146-199
54
2
1:146-199
2:146-199
54
54
[
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]
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1pd211 (1:76-199)
1b: SCOP_d1pd221 (2:76-199)
2a: SCOP_d1pd212 (1:1-75)
2b: SCOP_d1pd222 (2:1-75)
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)
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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
:
Class sigma GST
(12)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(1)
1a
d1pd211
1:76-199
1b
d1pd221
2:76-199
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thioredoxin fold
(994)
Superfamily
:
Thioredoxin-like
(992)
Family
:
Glutathione S-transferase (GST), N-terminal domain
(216)
Protein domain
:
Class sigma GST
(12)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(1)
2a
d1pd212
1:1-75
2b
d1pd222
2:1-75
[
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]
CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1pd2101 (1:1-75,1:184-199)
1b: CATH_1pd2201 (2:1-75,2:184-199)
2a: CATH_1pd2102 (1:76-183)
2b: CATH_1pd2202 (2:76-183)
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)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Glutaredoxin
(620)
Homologous Superfamily
:
Glutaredoxin
(617)
Norway rat (Rattus norvegicus)
(10)
1a
1pd2101
1:1-75,1:184-199
1b
1pd2201
2:1-75,2:184-199
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)
Norway rat (Rattus norvegicus)
(7)
2a
1pd2102
1:76-183
2b
1pd2202
2:76-183
[
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_GST_C_1pd2201 (2:86-185)
1b: PFAM_GST_C_1pd2202 (2:86-185)
2a: PFAM_GST_N_1pd2203 (2:4-73)
2b: PFAM_GST_N_1pd2204 (2:4-73)
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Clans
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(
)
Organisms
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)
(
)
Clan
:
GST_C
(118)
Family
:
GST_C
(102)
Rattus norvegicus (Rat)
(2)
1a
GST_C-1pd2201
2:86-185
1b
GST_C-1pd2202
2:86-185
Clan
:
Thioredoxin
(367)
Family
:
GST_N
(88)
Rattus norvegicus (Rat)
(2)
2a
GST_N-1pd2203
2:4-73
2b
GST_N-1pd2204
2:4-73
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