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1IYI
Biol. Unit 1
Info
Asym.Unit (159 KB)
Biol.Unit 1 (79 KB)
Biol.Unit 2 (79 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
Authors
:
T. Inoue
Date
:
26 Aug 02 (Deposition) - 08 Apr 03 (Release) - 16 Apr 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,C (1x)
Keywords
:
Hematopoietic Prostaglandin D Synthase, Pgds, Gst, Sigma-Class Gst, Ligase, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Inoue, D. Irikura, N. Okazaki, S. Kinugasa, H. Matsumura, N. Uodome M. Yamamoto, T. Kumasaka, M. Miyano, Y. Kai, Y. Urade
Mechanism Of Metal Activation Of Human Hematopoietic Prostaglandin D Synthase
Nat. Struct. Biol. V. 10 291 2003
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: CALCIUM ION (CAa)
1b: CALCIUM ION (CAb)
2a: GLUTATHIONE (GSHa)
2b: GLUTATHIONE (GSHb)
2c: GLUTATHIONE (GSHc)
2d: GLUTATHIONE (GSHd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CA
-1
Ligand/Ion
CALCIUM ION
2
GSH
2
Ligand/Ion
GLUTATHIONE
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:1259 , HOH A:1284 , HOH A:1437 , ASP D:696 , HOH D:1908 , HOH D:2009 , HOH D:2030
BINDING SITE FOR RESIDUE CA D 1900
2
AC3
SOFTWARE
TYR A:8 , ARG A:14 , TRP A:39 , LYS A:50 , ILE A:51 , GLN A:63 , SER A:64 , HOH A:1224 , HOH A:1225 , HOH A:1229 , HOH A:1254 , HOH A:1257 , HOH A:1419 , HOH A:1422 , ASP D:697
BINDING SITE FOR RESIDUE GSH A 1200
3
AC6
SOFTWARE
ASP A:97 , TYR D:608 , ARG D:614 , TRP D:639 , LYS D:643 , LYS D:650 , ILE D:651 , GLN D:663 , SER D:664 , HOH D:1910 , HOH D:1960 , HOH D:2015 , HOH D:2017 , HOH D:2043 , HOH D:2068 , HOH D:2119
BINDING SITE FOR RESIDUE GSH D 1800
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are only available for the asymmetric unit)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: GST_NTER (A:2-79,D:602-679)
2: GST_CTER (A:81-199,D:681-799)
;
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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
2
A:2-79
-
-
D:602-679
2
GST_CTER
PS50405
Soluble glutathione S-transferase C-terminal domain profile.
HPGDS_HUMAN
81-199
2
A:81-199
-
-
D:681-799
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d1iyia1 (A:76-199)
1b: SCOP_d1iyic1 (C:476-599)
1c: SCOP_d1iyid1 (D:676-799)
1d: SCOP_d1iyib1 (B:276-399)
2a: SCOP_d1iyia2 (A:2-75)
2b: SCOP_d1iyic2 (C:402-475)
2c: SCOP_d1iyid2 (D:602-675)
2d: SCOP_d1iyib2 (B:202-275)
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(
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)
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)
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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)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d1iyia1
A:76-199
1b
d1iyic1
C:476-599
1c
d1iyid1
D:676-799
1d
d1iyib1
B:276-399
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)
Human (Homo sapiens) [TaxId: 9606]
(7)
2a
d1iyia2
A:2-75
2b
d1iyic2
C:402-475
2c
d1iyid2
D:602-675
2d
d1iyib2
B:202-275
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1iyiA01 (A:2-75,A:184-199)
1b: CATH_1iyiB01 (B:203-277,B:386-399)
1c: CATH_1iyiC01 (C:403-477,C:586-599)
1d: CATH_1iyiD01 (D:603-677,D:786-799)
2a: CATH_1iyiA02 (A:76-183)
2b: CATH_1iyiB02 (B:278-385)
2c: CATH_1iyiC02 (C:478-585)
2d: CATH_1iyiD02 (D:678-785)
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)
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(
)
(
)
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
1iyiA01
A:2-75,A:184-199
1b
1iyiB01
B:203-277,B:386-399
1c
1iyiC01
C:403-477,C:586-599
1d
1iyiD01
D:603-677,D:786-799
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
1iyiA02
A:76-183
2b
1iyiB02
B:278-385
2c
1iyiC02
C:478-585
2d
1iyiD02
D:678-785
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Pfam Domains
(0, 0)
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Chain A
Chain D
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (159 KB)
Header - Asym.Unit
Biol.Unit 1 (79 KB)
Header - Biol.Unit 1
Biol.Unit 2 (79 KB)
Header - Biol.Unit 2
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