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1JEH
Asym. Unit
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Asym.Unit (156 KB)
Biol.Unit 1 (151 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF YEAST E3, LIPOAMIDE DEHYDROGENASE
Authors
:
T. Toyoda, K. Suzuki, T. Sekigushi, J. Reed, A. Takenaka
Date
:
18 Jun 01 (Deposition) - 11 Jul 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
2-Oxoglutarate Dehydrogenase Complex, Pyruvate Dehydrogenase Complex, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Toyoda, K. Suzuki, T. Sekiguchi, L. J. Reed, A. Takenaka
Crystal Structure Of Eucaryotic E3, Lipoamide Dehydrogenase From Yeast.
J. Biochem. (Tokyo) V. 123 668 1998
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: FLAVIN-ADENINE DINUCLEOTIDE (FADa)
1b: FLAVIN-ADENINE DINUCLEOTIDE (FADb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
FAD
2
Ligand/Ion
FLAVIN-ADENINE DINUCLEOTIDE
[
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]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ILE A:11 , GLY A:12 , GLY A:14 , PRO A:15 , ALA A:16 , VAL A:34 , GLU A:35 , LYS A:36 , ARG A:37 , GLY A:42 , THR A:43 , CYS A:44 , VAL A:47 , GLY A:48 , CYS A:49 , SER A:52 , LYS A:53 , GLY A:118 , ALA A:152 , THR A:153 , GLY A:154 , SER A:173 , ILE A:194 , ARG A:285 , TYR A:288 , GLY A:291 , LEU A:292 , GLY A:324 , ASP A:325 , MET A:331 , LEU A:332 , ALA A:333 , HIS A:334 , TYR A:364 , HIS B:457 , PRO B:458
BINDING SITE FOR RESIDUE FAD A 480
2
AC2
SOFTWARE
HIS A:457 , PRO A:458 , ILE B:11 , GLY B:12 , GLY B:14 , PRO B:15 , ALA B:16 , GLU B:35 , LYS B:36 , ARG B:37 , GLY B:42 , THR B:43 , CYS B:44 , GLY B:48 , CYS B:49 , SER B:52 , LYS B:53 , ASN B:117 , GLY B:118 , ALA B:152 , THR B:153 , GLY B:154 , SER B:155 , SER B:173 , ARG B:285 , TYR B:288 , ALA B:290 , GLY B:291 , LEU B:292 , GLY B:324 , ASP B:325 , MET B:331 , LEU B:332 , ALA B:333 , HIS B:334 , TYR B:364 , HOH B:611
BINDING SITE FOR RESIDUE FAD B 580
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PYRIDINE_REDOX_1 (A:41-51,B:41-51)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PYRIDINE_REDOX_1
PS00076
Pyridine nucleotide-disulphide oxidoreductases class-I active site.
DLDH_YEAST
62-72
2
A:41-51
B:41-51
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Exons
(1, 2)
Info
All Exons
Exon 1.1 (A:1-478 | B:1-478)
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All Exon Boundaries
1: Boundary -/1.1
2: Boundary 1.1/-
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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
1.1
YFL018C
1
YFL018C.1
VI:103121-101622
1500
DLDH_YEAST
1-499
499
2
A:1-478
B:1-478
478
478
[
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]
SCOP Domains
(2, 6)
Info
All SCOP Domains
1a: SCOP_d1jeha3 (A:356-478)
1b: SCOP_d1jehb3 (B:356-478)
2a: SCOP_d1jeha1 (A:1-160,A:283-355)
2b: SCOP_d1jeha2 (A:161-282)
2c: SCOP_d1jehb1 (B:1-160,B:283-355)
2d: SCOP_d1jehb2 (B:161-282)
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)
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)
(
)
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)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
CO dehydrogenase flavoprotein C-domain-like
(111)
Superfamily
:
FAD/NAD-linked reductases, dimerisation (C-terminal) domain
(76)
Family
:
FAD/NAD-linked reductases, dimerisation (C-terminal) domain
(76)
Protein domain
:
Dihydrolipoamide dehydrogenase
(10)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
1a
d1jeha3
A:356-478
1b
d1jehb3
B:356-478
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
FAD/NAD(P)-binding domain
(331)
Superfamily
:
FAD/NAD(P)-binding domain
(331)
Family
:
FAD/NAD-linked reductases, N-terminal and central domains
(92)
Protein domain
:
Dihydrolipoamide dehydrogenase
(10)
Baker's yeast (Saccharomyces cerevisiae) [TaxId: 4932]
(2)
2a
d1jeha1
A:1-160,A:283-355
2b
d1jeha2
A:161-282
2c
d1jehb1
B:1-160,B:283-355
2d
d1jehb2
B:161-282
[
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]
CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_1jehA03 (A:358-478)
1b: CATH_1jehB03 (B:358-478)
2a: CATH_1jehA01 (A:3-157,A:284-357)
2b: CATH_1jehB01 (B:3-157,B:284-357)
2c: CATH_1jehA02 (A:158-283)
2d: CATH_1jehB02 (B:158-283)
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Enolase-like; domain 1
(252)
Homologous Superfamily
:
[code=3.30.390.30, no name defined]
(99)
Baker's yeast (Saccharomyces cerevisiae)
(3)
1a
1jehA03
A:358-478
1b
1jehB03
B:358-478
Architecture
:
3-Layer(bba) Sandwich
(528)
Topology
:
FAD/NAD(P)-binding domain
(373)
Homologous Superfamily
:
[code=3.50.50.60, no name defined]
(373)
Baker's yeast (Saccharomyces cerevisiae)
(22)
2a
1jehA01
A:3-157,A:284-357
2b
1jehB01
B:3-157,B:284-357
2c
1jehA02
A:158-283
2d
1jehB02
B:158-283
[
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Pfam Domains
(3, 6)
Info
all PFAM domains
1a: PFAM_Pyr_redox_1jehB01 (B:185-270)
1b: PFAM_Pyr_redox_1jehB02 (B:185-270)
2a: PFAM_Pyr_redox_2_1jehB03 (B:7-331)
2b: PFAM_Pyr_redox_2_1jehB04 (B:7-331)
3a: PFAM_Pyr_redox_dim_1jehB05 (B:359-468)
3b: PFAM_Pyr_redox_dim_1jehB06 (B:359-468)
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)
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)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
Pyr_redox
(62)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
1a
Pyr_redox-1jehB01
B:185-270
1b
Pyr_redox-1jehB02
B:185-270
Family
:
Pyr_redox_2
(69)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
2a
Pyr_redox_2-1jehB03
B:7-331
2b
Pyr_redox_2-1jehB04
B:7-331
Clan
:
no clan defined [family: Pyr_redox_dim]
(44)
Family
:
Pyr_redox_dim
(44)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(2)
3a
Pyr_redox_dim-1jehB05
B:359-468
3b
Pyr_redox_dim-1jehB06
B:359-468
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