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2CVD
Biol. Unit 2
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:
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Gene Ontology, PubMed, Web (Google)
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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
(3, 10)
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
6
Ligand/Ion
GLYCEROL
2
GSH
2
Ligand/Ion
GLUTATHIONE
3
HQL
2
Ligand/Ion
4-(BENZHYDRYLOXY)-1-[3-(1H-TETRAAZOL-5-YL)PROPYL]PIPERIDINE
4
MG
-1
Ligand/Ion
MAGNESIUM ION
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Sites
(11, 11)
Info
All Sites
01: AC2 (SOFTWARE)
02: AC4 (SOFTWARE)
03: AC5 (SOFTWARE)
04: AC8 (SOFTWARE)
05: AC9 (SOFTWARE)
06: BC2 (SOFTWARE)
07: BC3 (SOFTWARE)
08: BC4 (SOFTWARE)
09: BC5 (SOFTWARE)
10: BC6 (SOFTWARE)
11: BC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
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
02
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
03
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
04
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
05
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
06
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
07
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
08
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
09
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
10
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
11
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 only available for the asymmetric unit)
All SNPs/Variants
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: GST_NTER (B:2-79,C:2-79)
2: GST_CTER (B:81-199,C: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_HUMAN
2-79
2
-
B:2-79
C:2-79
-
2
GST_CTER
PS50405
Soluble glutathione S-transferase C-terminal domain profile.
HPGDS_HUMAN
81-199
2
-
B:81-199
C:81-199
-
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Exons
(0, 0)
Info
All Exons
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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_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)
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Protein Domains
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(
)
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)
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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
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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Asymmetric Unit 1
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