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2CVD
Asym. Unit
Info
Asym.Unit (169 KB)
Biol.Unit 1 (84 KB)
Biol.Unit 2 (83 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF HUMAN HEMATOPOIETIC PROSTAGLANDIN D SYNTHASE COMPLEXED WITH HQL-79
Authors
:
K. Aritake, Y. Kado, T. Inoue, M. Miyano, Y. Urade
Date
:
02 Jun 05 (Deposition) - 18 Apr 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.45
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,D (1x)
Biol. Unit 2: B,C (1x)
Keywords
:
Glutathione-S-Transferase, Isomerase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Aritake, Y. Kado, T. Inoue, M. Miyano, Y. Urade
Structural And Functional Characterization Of Hql-79, An Orally Selective Inhibitor Of Human Hematopoietic Prostaglandin D Synthase.
J. Biol. Chem. V. 281 15277 2006
[
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Hetero Components
(4, 17)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
2a: GLUTATHIONE (GSHa)
2b: GLUTATHIONE (GSHb)
2c: GLUTATHIONE (GSHc)
2d: GLUTATHIONE (GSHd)
3a: 4-(BENZHYDRYLOXY)-1-[3-(1H-TETRAAZ... (HQLa)
3b: 4-(BENZHYDRYLOXY)-1-[3-(1H-TETRAAZ... (HQLb)
3c: 4-(BENZHYDRYLOXY)-1-[3-(1H-TETRAAZ... (HQLc)
3d: 4-(BENZHYDRYLOXY)-1-[3-(1H-TETRAAZ... (HQLd)
4a: MAGNESIUM ION (MGa)
4b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
7
Ligand/Ion
GLYCEROL
2
GSH
4
Ligand/Ion
GLUTATHIONE
3
HQL
4
Ligand/Ion
4-(BENZHYDRYLOXY)-1-[3-(1H-TETRAAZOL-5-YL)PROPYL]PIPERIDINE
4
MG
2
Ligand/Ion
MAGNESIUM ION
[
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Sites
(17, 17)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:4142 , HOH A:4143 , HOH A:4144 , HOH D:2989 , HOH D:2990 , HOH D:2991
BINDING SITE FOR RESIDUE MG A 4001
02
AC2
SOFTWARE
HOH B:4126 , HOH B:4127 , HOH B:4183 , HOH C:3179 , HOH C:3180 , HOH C:3181
BINDING SITE FOR RESIDUE MG B 4002
03
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 , HQL A:2201 , HOH A:4003 , HOH A:4009 , HOH A:4045 , HOH A:4048 , HOH A:4130 , ASP D:97
BINDING SITE FOR RESIDUE GSH A 2001
04
AC4
SOFTWARE
TYR B:8 , ARG B:14 , TRP B:39 , LYS B:43 , LYS B:50 , ILE B:51 , GLN B:63 , SER B:64 , HOH B:4012 , HOH B:4016 , HOH B:4031 , HOH B:4069 , HOH B:4097 , HOH B:4103 , ASP C:97
BINDING SITE FOR RESIDUE GSH B 2002
05
AC5
SOFTWARE
ASP B:97 , TYR C:8 , ARG C:14 , TRP C:39 , LYS C:43 , LYS C:50 , ILE C:51 , GLN C:63 , SER C:64 , HOH C:3005 , HOH C:3020 , HOH C:3088 , HOH C:3153 , HOH C:3263 , HOH C:3318
BINDING SITE FOR RESIDUE GSH C 2003
06
AC6
SOFTWARE
ASP A:97 , TYR D:8 , ARG D:14 , TRP D:39 , LYS D:43 , LYS D:50 , ILE D:51 , GLN D:63 , SER D:64 , HOH D:2804 , HOH D:2821 , HOH D:2868 , HOH D:2948 , HOH D:2957
BINDING SITE FOR RESIDUE GSH D 2004
07
AC7
SOFTWARE
TYR A:8 , MET A:11 , GLY A:13 , MET A:99 , PHE A:102 , TRP A:104 , TYR A:152 , THR A:159 , GSH A:2001 , HOH A:4246
BINDING SITE FOR RESIDUE HQL A 2201
08
AC8
SOFTWARE
HOH A:4327 , TYR B:8 , MET B:11 , GLY B:13 , MET B:99 , PHE B:102 , TRP B:104 , TYR B:152 , THR B:159 , LEU B:199 , HOH B:4217
BINDING SITE FOR RESIDUE HQL B 2401
09
AC9
SOFTWARE
TYR C:8 , MET C:11 , GLY C:13 , ARG C:14 , MET C:99 , PHE C:102 , TRP C:104 , TYR C:152 , THR C:159 , HOH C:3238 , HOH C:3317
BINDING SITE FOR RESIDUE HQL C 2601
10
BC1
SOFTWARE
MET D:11 , GLY D:13 , ARG D:14 , MET D:99 , PHE D:102 , TRP D:104 , TYR D:152 , THR D:159 , HOH D:3095
BINDING SITE FOR RESIDUE HQL D 2801
11
BC2
SOFTWARE
GLN C:28 , TYR C:29 , GOL C:3002 , HOH C:3084 , HOH C:3188 , HOH C:3280 , ARG D:12 , THR D:197 , HOH D:2824 , HOH D:2827 , HOH D:2918
BINDING SITE FOR RESIDUE GOL C 3001
12
BC3
SOFTWARE
GLN C:28 , TYR C:29 , TRP C:190 , GOL C:3001 , HOH C:3041 , HOH C:3174 , LYS D:198
BINDING SITE FOR RESIDUE GOL C 3002
13
BC4
SOFTWARE
ARG C:12 , THR C:197 , GOL C:3004 , HOH C:3033 , HOH C:3043 , HOH C:3070 , GLN D:28 , TYR D:29 , HOH D:3053
BINDING SITE FOR RESIDUE GOL C 3003
14
BC5
SOFTWARE
LYS C:198 , GOL C:3003 , HOH C:3234 , GLN D:28 , TYR D:29 , HOH D:2839 , HOH D:3000
BINDING SITE FOR RESIDUE GOL C 3004
15
BC6
SOFTWARE
GLN B:28 , TYR B:29 , TRP B:190 , ARG B:193 , HOH B:4067 , HOH B:4078 , HOH B:4187
BINDING SITE FOR RESIDUE GOL B 3005
16
BC7
SOFTWARE
GLU A:84 , HIS A:87 , ILE A:142 , GLY A:143 , HOH A:4075 , TYR D:122
BINDING SITE FOR RESIDUE GOL A 3006
17
BC8
SOFTWARE
ASP B:130 , HOH B:4100 , LYS C:43 , SER C:44 , LEU C:46 , HOH C:3271 , HOH C:3272 , HOH C:3347
BINDING SITE FOR RESIDUE GOL B 3007
[
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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:76-112 | 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:
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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
[
close EXON info
]
SCOP Domains
(2, 8)
Info
All SCOP Domains
1a: SCOP_d2cvda1 (A:76-199)
1b: SCOP_d2cvdb1 (B:76-199)
1c: SCOP_d2cvdc1 (C:76-199)
1d: SCOP_d2cvdd1 (D:76-199)
2a: SCOP_d2cvda2 (A:2-75)
2b: SCOP_d2cvdb2 (B:2-75)
2c: SCOP_d2cvdc2 (C:2-75)
2d: SCOP_d2cvdd2 (D:2-75)
View:
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Classes
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)
(
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Folds
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(
)
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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
:
Class sigma GST
(12)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d2cvda1
A:76-199
1b
d2cvdb1
B:76-199
1c
d2cvdc1
C:76-199
1d
d2cvdd1
D: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)
Human (Homo sapiens) [TaxId: 9606]
(7)
2a
d2cvda2
A:2-75
2b
d2cvdb2
B:2-75
2c
d2cvdc2
C:2-75
2d
d2cvdd2
D:2-75
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2cvdA01 (A:2-75,A:184-199)
1b: CATH_2cvdB01 (B:2-75,B:184-199)
1c: CATH_2cvdC01 (C:2-75,C:184-199)
1d: CATH_2cvdD01 (D:2-75,D:184-199)
2a: CATH_2cvdA02 (A:76-183)
2b: CATH_2cvdB02 (B:76-183)
2c: CATH_2cvdC02 (C:76-183)
2d: CATH_2cvdD02 (D:76-183)
View:
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Topologies
(
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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
2cvdA01
A:2-75,A:184-199
1b
2cvdB01
B:2-75,B:184-199
1c
2cvdC01
C:2-75,C:184-199
1d
2cvdD01
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
2cvdA02
A:76-183
2b
2cvdB02
B:76-183
2c
2cvdC02
C:76-183
2d
2cvdD02
D:76-183
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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