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1V40
Biol. Unit 1
Info
Asym.Unit (174 KB)
Biol.Unit 1 (87 KB)
Biol.Unit 2 (84 KB)
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(1)
Title
:
FIRST INHIBITOR COMPLEX STRUCTURE OF HUMAN HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE
Authors
:
T. Inoue, Y. Okano, Y. Kado, K. Aritake, D. Irikura, N. Uodome, S. Kinuga N. Okazaki, H. Matsumura, Y. Kai, Y. Urade
Date
:
07 Nov 03 (Deposition) - 07 Nov 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
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-2 Class Gst, Ligase, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Inoue, Y. Okano, Y. Kado, K. Aritake, D. Irikura, N. Uodome, N. Okazaki, S. Kinugasa, H. Shishitani, H. Matsumura, Y. Kai, Y. Urade
First Determination Of The Inhibitor Complex Structure Of Human Hematopoietic Prostaglandin D Synthase.
J. Biochem. (Tokyo) V. 135 279 2004
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Hetero Components
(3, 7)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
2a: GLUTATHIONE (GSHa)
2b: GLUTATHIONE (GSHb)
2c: GLUTATHIONE (GSHc)
2d: GLUTATHIONE (GSHd)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
4a: 3-(1,3-BENZOTHIAZOL-2-YL)-2-(1,4-D... (O16a)
4b: 3-(1,3-BENZOTHIAZOL-2-YL)-2-(1,4-D... (O16b)
4c: 3-(1,3-BENZOTHIAZOL-2-YL)-2-(1,4-D... (O16c)
4d: 3-(1,3-BENZOTHIAZOL-2-YL)-2-(1,4-D... (O16d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
3
Ligand/Ion
GLYCEROL
2
GSH
2
Ligand/Ion
GLUTATHIONE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
O16
2
Ligand/Ion
3-(1,3-BENZOTHIAZOL-2-YL)-2-(1,4-DIOXO-1,2,3,4-TETRAHYDROPHTHALAZIN-6-YL)-5-[(E)-2-PHENYLVINYL]-3H-TETRAAZOL-2-IUM
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Sites
(10, 10)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC3 (SOFTWARE)
03: AC6 (SOFTWARE)
04: AC7 (SOFTWARE)
05: BC1 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:4129 , HOH A:4174 , HOH A:4290 , HOH D:3999 , HOH D:4095 , HOH D:4096
BINDING SITE FOR RESIDUE MG A 3900
02
AC3
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 , O16 A:3201 , HOH A:3953 , HOH A:3959 , HOH A:4117 , HOH A:4289 , ASP D:697
BINDING SITE FOR RESIDUE GSH A 3200
03
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:3822 , HOH D:3867 , HOH D:3872 , HOH D:4058
BINDING SITE FOR RESIDUE GSH D 3800
04
AC7
SOFTWARE
PHE A:9 , ARG A:14 , MET A:99 , TRP A:104 , ALA A:105 , TYR A:152 , CYS A:156 , LEU A:199 , GSH A:3200
BINDING SITE FOR RESIDUE O16 A 3201
05
BC1
SOFTWARE
HOH A:4258 , GLY D:613 , ARG D:614 , ASP D:696 , MET D:699 , TRP D:704 , ALA D:705 , TYR D:752 , LEU D:799 , HOH D:4090
BINDING SITE FOR RESIDUE O16 D 3801
06
BC2
SOFTWARE
LYS A:43 , PHE A:48 , GLY A:49 , HOH A:3991 , HOH A:4119 , HOH A:4126 , HOH A:4287 , HIS D:726 , ASP D:730 , HOH D:3804
BINDING SITE FOR RESIDUE GOL A 3001
07
BC3
SOFTWARE
GLU A:84 , TYR A:134 , ARG A:138 , LEU A:141 , ILE A:142 , GLY A:143 , HOH A:4029 , HOH A:4142 , HOH A:4260 , HOH A:4311 , TYR D:722
BINDING SITE FOR RESIDUE GOL A 3002
08
BC4
SOFTWARE
GLN C:428 , TYR C:429 , GLN D:796 , THR D:797 , LYS D:798 , HOH D:3904 , HOH D:3905 , HOH D:3991 , HOH D:3992 , HOH D:3993
BINDING SITE FOR RESIDUE GOL C 3003
09
BC5
SOFTWARE
THR C:597 , HOH C:3735 , HOH C:3737 , HOH C:3741 , HOH C:3744 , HOH C:3745 , GLN D:628 , TYR D:629 , GOL D:3005
BINDING SITE FOR RESIDUE GOL C 3004
10
BC6
SOFTWARE
LYS C:598 , GOL C:3004 , GLN D:628 , TYR D:629 , TRP D:790 , HOH D:3891 , HOH D:3892
BINDING SITE FOR RESIDUE GOL D 3005
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
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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 (A:2-79,D:602-679)
2: GST_CTER (A:81-199,D:681-799)
;
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
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)
Info
All Exons
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All Exon Boundaries
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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_d1v40a1 (A:76-199)
1b: SCOP_d1v40b1 (B:276-399)
1c: SCOP_d1v40c1 (C:476-599)
1d: SCOP_d1v40d1 (D:676-799)
2a: SCOP_d1v40a2 (A:2-75)
2b: SCOP_d1v40b2 (B:202-275)
2c: SCOP_d1v40c2 (C:402-475)
2d: SCOP_d1v40d2 (D:602-675)
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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
d1v40a1
A:76-199
1b
d1v40b1
B:276-399
1c
d1v40c1
C:476-599
1d
d1v40d1
D:676-799
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
d1v40a2
A:2-75
2b
d1v40b2
B:202-275
2c
d1v40c2
C:402-475
2d
d1v40d2
D:602-675
[
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CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_1v40A01 (A:2-75,A:184-199)
1b: CATH_1v40B01 (B:202-275,B:384-399)
1c: CATH_1v40C01 (C:402-475,C:584-599)
1d: CATH_1v40D01 (D:602-675,D:784-799)
2a: CATH_1v40A02 (A:76-183)
2b: CATH_1v40B02 (B:276-383)
2c: CATH_1v40C02 (C:476-583)
2d: CATH_1v40D02 (D:676-783)
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Topologies
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Homologous Superfamilies
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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
1v40A01
A:2-75,A:184-199
1b
1v40B01
B:202-275,B:384-399
1c
1v40C01
C:402-475,C:584-599
1d
1v40D01
D:602-675,D:784-799
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
1v40A02
A:76-183
2b
1v40B02
B:276-383
2c
1v40C02
C:476-583
2d
1v40D02
D:676-783
[
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Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_GST_C_1v40D01 (D:681-785)
1b: PFAM_GST_C_1v40D02 (D:681-785)
1c: PFAM_GST_C_1v40D03 (D:681-785)
1d: PFAM_GST_C_1v40D04 (D:681-785)
2a: PFAM_GST_N_1v40D05 (D:604-673)
2b: PFAM_GST_N_1v40D06 (D:604-673)
2c: PFAM_GST_N_1v40D07 (D:604-673)
2d: PFAM_GST_N_1v40D08 (D:604-673)
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Clans
(
)
(
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Families
(
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(
)
Organisms
(
)
(
)
Clan
:
GST_C
(118)
Family
:
GST_C
(102)
Homo sapiens (Human)
(47)
1a
GST_C-1v40D01
D:681-785
1b
GST_C-1v40D02
D:681-785
1c
GST_C-1v40D03
D:681-785
1d
GST_C-1v40D04
D:681-785
Clan
:
Thioredoxin
(367)
Family
:
GST_N
(88)
Homo sapiens (Human)
(45)
2a
GST_N-1v40D05
D:604-673
2b
GST_N-1v40D06
D:604-673
2c
GST_N-1v40D07
D:604-673
2d
GST_N-1v40D08
D:604-673
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Asymmetric Unit 1
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Asym.Unit (174 KB)
Header - Asym.Unit
Biol.Unit 1 (87 KB)
Header - Biol.Unit 1
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Header - Biol.Unit 2
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