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2DM6
Asym. Unit
Info
Asym.Unit (124 KB)
Biol.Unit 1 (119 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF ANTI-CONFIGURATION OF INDOMETHACIN AND LEUKOTRIENE B4 12-HYDROXYDEHYDROGENASE/15-OXO-PROSTAGLANDIN 13-REDUCTASE COMPLEX
Authors
:
T. Hori, J. Ishijima, T. Yokomizo, H. Ago, T. Shimizu, M. Miyano, Riken Structural Genomics/Proteomics Initiative (Rsgi)
Date
:
20 Apr 06 (Deposition) - 28 Nov 06 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Nad(P)-Binding Rossmann-Fold Domains, Riken Structural Genomics/Proteomics Initiative, Rsgi, Structural Genomics, Oxidoreductase
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
T. Hori, J. Ishijima, T. Yokomizo, H. Ago, T. Shimizu, M. Miyano
Crystal Structure Of Anti-Configuration Of Indomethacin And Leukotriene B4 12-Hydroxydehydrogenase/15-Oxo-Prostaglandin 13-Reductase Complex Reveals The Structural Basis Of Broad Spectrum Indomethacin Efficacy
J. Biochem. (Tokyo) V. 140 457 2006
(for further references see the
PDB file header
)
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: INDOMETHACIN (IMNa)
2a: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPa)
2b: NADP NICOTINAMIDE-ADENINE-DINUCLEO... (NAPb)
3a: TRIS(HYDROXYETHYL)AMINOMETHANE (TAMa)
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No.
Name
Count
Type
Full Name
1
IMN
1
Ligand/Ion
INDOMETHACIN
2
NAP
2
Ligand/Ion
NADP NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
3
TAM
1
Ligand/Ion
TRIS(HYDROXYETHYL)AMINOMETHANE
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PRO A:48 , MET A:124 , THR A:128 , GLY A:152 , ALA A:153 , VAL A:154 , ALA A:173 , GLY A:174 , LYS A:178 , TYR A:193 , ASN A:217 , VAL A:218 , CYS A:239 , GLY A:240 , ALA A:241 , 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 , HOH A:1403 , HOH A:1405 , HOH A:1412 , HOH A:1421 , HOH A:1422 , HOH A:1428 , HOH A:1443 , HOH A:1488 , HOH A:1574 , HOH A:1613 , HOH A:1619
BINDING SITE FOR RESIDUE NAP A 1400
2
AC2
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 , HOH B:5005 , HOH B:5006 , HOH B:5011 , HOH B:5034 , HOH B:5066 , HOH B:5079 , HOH B:5081 , HOH B:5083 , HOH B:5188 , HOH B:5195 , HOH B:5198 , HOH B:5291
BINDING SITE FOR RESIDUE NAP B 2400
3
AC3
SOFTWARE
TYR A:49 , ILE A:52 , ALA A:53 , ARG A:56 , TYR A:245 , ILE A:271 , HOH A:1566 , GLU B:258 , ILE B:261 , TYR B:262
BINDING SITE FOR RESIDUE IMN A 1401
4
AC4
SOFTWARE
GLU A:307 , LYS B:304 , GLU B:307 , ASN B:308 , HOH B:5252
BINDING SITE FOR RESIDUE TAM B 5000
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SAPs(SNPs)/Variants
(0, 0)
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(mutated residues are not available)
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PROSITE Patterns/Profiles
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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.
SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d2dm6a1 (A:-2-112,A:295-329)
1b: SCOP_d2dm6b1 (B:-4-112,B:295-329)
2a: SCOP_d2dm6a2 (A:113-294)
2b: SCOP_d2dm6b2 (B:113-294)
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Classes
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)
(
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Folds
(
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(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d2dm6a1
A:-2-112,A:295-329
1b
d2dm6b1
B:-4-112,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
d2dm6a2
A:113-294
2b
d2dm6b2
B:113-294
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_2dm6A02 (A:121-298)
1b: CATH_2dm6B02 (B:121-298)
2a: CATH_2dm6B01 (B:-4-120,B:299-329)
2b: CATH_2dm6A01 (A:-2-120,A:299-329)
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)
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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
2dm6A02
A:121-298
1b
2dm6B02
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
2dm6B01
B:-4-120,B:299-329
2b
2dm6A01
A:-2-120,A:299-329
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Pfam Domains
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Asymmetric Unit 1
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Asym.Unit (124 KB)
Header - Asym.Unit
Biol.Unit 1 (119 KB)
Header - Biol.Unit 1
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