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1V3V
Asym. Unit
Info
Asym.Unit (129 KB)
Biol.Unit 1 (125 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE/15-OXO-PROSTAGLANDIN 13-REDUCTASE COMPLEXED WITH NADP AND 15-OXO-PGE2
Authors
:
T. Hori, T. Yokomizo, H. Ago, M. Sugahara, G. Ueno, M. Yamamoto, T. Kumasaka, T. Shimizu, M. Miyano, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
06 Nov 03 (Deposition) - 13 Jul 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Rossmann Fold, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Hori, T. Yokomizo, H. Ago, M. Sugahara, G. Ueno, M. Yamamoto, T. Kumasaka, T. Shimizu, M. Miyano
Structural Basis Of Leukotriene B4 12-Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Catalytic Mechanism And A Possible Src Homology 3 Domain Binding Loop
J. Biol. Chem. V. 279 22615 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 10)
Info
All Hetero Components
1a: (5E,13E)-11-HYDROXY-9,15-DIOXOPROS... (5OPa)
1b: (5E,13E)-11-HYDROXY-9,15-DIOXOPROS... (5OPb)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
3a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
3b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
5OP
2
Ligand/Ion
(5E,13E)-11-HYDROXY-9,15-DIOXOPROSTA-5,13-DIEN-1-OICACID
2
CL
6
Ligand/Ion
CHLORIDE ION
3
NAP
2
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
[
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Sites
(10, 10)
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)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HIS B:12 , PHE B:13 , SER B:54 , LYS B:55
BINDING SITE FOR RESIDUE CL B 1001
02
AC2
SOFTWARE
GLU B:315 , ASN B:318 , HOH B:2533 , HOH B:2552 , HOH B:2556
BINDING SITE FOR RESIDUE CL B 1002
03
AC3
SOFTWARE
ASN A:318 , HOH A:1501
BINDING SITE FOR RESIDUE CL A 1003
04
AC4
SOFTWARE
HIS A:12 , PHE A:13 , SER A:54 , LYS A:55
BINDING SITE FOR RESIDUE CL A 1004
05
AC5
SOFTWARE
ARG A:51 , HOH A:1418 , HOH A:1760
BINDING SITE FOR RESIDUE CL A 1005
06
AC6
SOFTWARE
GLY B:15 , ARG B:51 , ASN B:246 , HOH B:2410
BINDING SITE FOR RESIDUE CL B 1006
07
AC7
SOFTWARE
PRO A:48 , MET A:124 , THR A:128 , GLY A:152 , ALA A:153 , VAL A:154 , GLY A:174 , LYS A:178 , TYR A:193 , ASN A:217 , VAL A:218 , CYS A:239 , GLY A:240 , ILE A:242 , SER A:243 , TYR A:245 , PHE A:270 , ILE A:271 , VAL A:272 , MET A:316 , LEU A:317 , GLY A:319 , ASN A:321 , 5OP A:1360 , HOH A:1361 , HOH A:1363 , HOH A:1364 , HOH A:1366 , HOH A:1369 , HOH A:1401 , HOH A:1406 , HOH A:1426 , HOH A:1626 , HOH A:1632 , HOH A:1687
BINDING SITE FOR RESIDUE NAP A 1350
08
AC8
SOFTWARE
PRO B:48 , MET B:124 , THR B:128 , GLY B:152 , ALA B:153 , VAL B:154 , ALA B:173 , GLY B:174 , LYS B:178 , TYR B:193 , ASN B:217 , VAL B:218 , CYS B:239 , GLY B:240 , ILE B:242 , SER B:243 , TYR B:245 , PHE B:270 , ILE B:271 , VAL B:272 , MET B:316 , LEU B:317 , GLY B:319 , ASN B:321 , 5OP B:2360 , HOH B:2366 , HOH B:2367 , HOH B:2368 , HOH B:2372 , HOH B:2379 , HOH B:2391 , HOH B:2475 , HOH B:2520 , HOH B:2522 , HOH B:2524 , HOH B:2603 , HOH B:2683
BINDING SITE FOR RESIDUE NAP B 2350
09
AC9
SOFTWARE
TYR A:49 , TYR A:245 , TYR A:273 , NAP A:1350 , HOH A:1379 , GLU B:258 , ILE B:261 , TYR B:262
BINDING SITE FOR RESIDUE 5OP A 1360
10
BC1
SOFTWARE
GLU A:258 , ILE A:261 , TYR A:262 , TYR B:49 , TYR B:245 , TYR B:273 , NAP B:2350 , HOH B:2395
BINDING SITE FOR RESIDUE 5OP B 2360
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
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PROSITE Patterns/Profiles
(0, 0)
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d1v3va1 (A:1-112,A:295-329)
1b: SCOP_d1v3vb1 (B:2-112,B:295-329)
2a: SCOP_d1v3va2 (A:113-294)
2b: SCOP_d1v3vb2 (B:113-294)
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(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
GroES-like
(132)
Superfamily
:
GroES-like
(130)
Family
:
Alcohol dehydrogenase-like, N-terminal domain
(114)
Protein domain
:
Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase
(4)
Guinea pig (Cavia porcellus) [TaxId: 10141]
(4)
1a
d1v3va1
A:1-112,A:295-329
1b
d1v3vb1
B:2-112,B:295-329
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
NAD(P)-binding Rossmann-fold domains
(1604)
Superfamily
:
NAD(P)-binding Rossmann-fold domains
(1604)
Family
:
Alcohol dehydrogenase-like, C-terminal domain
(115)
Protein domain
:
Leukotriene b4 12-hydroxydehydrogenase/prostaglandin 15-keto reductase
(4)
Guinea pig (Cavia porcellus) [TaxId: 10141]
(4)
2a
d1v3va2
A:113-294
2b
d1v3vb2
B:113-294
[
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_1v3vA02 (A:121-298)
1b: CATH_1v3vB02 (B:121-298)
2a: CATH_1v3vA01 (A:-4-120,A:299-329)
2b: CATH_1v3vB01 (B:2-120,B:299-329)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
NAD(P)-binding Rossmann-like Domain
(1244)
Domestic guinea pig (Cavia porcellus)
(5)
1a
1v3vA02
A:121-298
1b
1v3vB02
B:121-298
Architecture
:
Alpha-Beta Complex
(3881)
Topology
:
Quinone Oxidoreductase; Chain A, domain 1
(131)
Homologous Superfamily
:
Medium-chain alcohol dehydrogenases, catalytic domain
(131)
Domestic guinea pig (Cavia porcellus)
(4)
2a
1v3vA01
A:-4-120,A:299-329
2b
1v3vB01
B:2-120,B:299-329
[
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_ADH_zinc_N_1v3vB01 (B:153-289)
1b: PFAM_ADH_zinc_N_1v3vB02 (B:153-289)
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)
Clan
:
NADP_Rossmann
(1239)
Family
:
ADH_zinc_N
(75)
Cavia porcellus (Guinea pig)
(3)
1a
ADH_zinc_N-1v3vB01
B:153-289
1b
ADH_zinc_N-1v3vB02
B:153-289
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Asymmetric Unit 1
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Asym.Unit (129 KB)
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