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3DVA
Asym. Unit
Info
Asym.Unit (888 KB)
Biol.Unit 1 (446 KB)
Biol.Unit 2 (439 KB)
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(1)
Title
:
SNAPSHOTS OF CATALYSIS IN THE E1 SUBUNIT OF THE PYRUVATE DEHYDROGENASE MULTI-ENZYME COMPLEX
Authors
:
X. Y. Pei, C. M. Titman, R. A. W. Frank, F. J. Leeper, B. F. Luisi
Date
:
18 Jul 08 (Deposition) - 13 Jan 09 (Release) - 13 Jan 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.35
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,I (1x)
Biol. Unit 2: E,F,G,H,J (1x)
Keywords
:
Oxidoreductase, Pyruvate, Dehydrogenase, Dihydrolipoyl, Acetyl Transferase, Multienzyme Complex, Transferase, Glycolysis, Phosphoprotein, Thiamine Pyrophosphate, Acyltransferase, Oxidoreductase/Transferase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
X. Y. Pei, C. M. Titman, R. A. Frank, F. J. Leeper, B. F. Luisi
Snapshots Of Catalysis In The E1 Subunit Of The Pyruvate Dehydrogenase Multienzyme Complex
Structure V. 16 1860 2008
(for further references see the
PDB file header
)
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
3a: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPWa)
3b: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPWb)
3c: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPWc)
3d: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPWd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
2
Ligand/Ion
POTASSIUM ION
2
MG
6
Ligand/Ion
MAGNESIUM ION
3
TPW
4
Ligand/Ion
2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE
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Sites
(12, 12)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:173 , ASN A:202 , PHE A:204 , TPW A:1370 , HOH A:1410
BINDING SITE FOR RESIDUE MG A1368
02
AC2
SOFTWARE
ILE B:112 , THR B:113 , ALA B:160 , ASP B:163 , ASP B:165 , HOH B:1363
BINDING SITE FOR RESIDUE K B1325
03
AC3
SOFTWARE
HOH A:1421 , HOH B:1335 , HOH C:1420 , HOH C:1483
BINDING SITE FOR RESIDUE MG A1326
04
AC4
SOFTWARE
ASP C:173 , ASN C:202 , PHE C:204 , TPW C:1370 , HOH C:1432
BINDING SITE FOR RESIDUE MG C1368
05
AC5
SOFTWARE
ILE D:112 , THR D:113 , ALA D:160 , ASP D:163 , ASP D:165 , HOH D:1474
BINDING SITE FOR RESIDUE K D1325
06
AC6
SOFTWARE
ASP G:173 , ASN G:202 , PHE G:204 , TPW G:1370 , HOH G:1407
BINDING SITE FOR RESIDUE MG G 369
07
AC7
SOFTWARE
GLY E:172 , ASP E:173 , GLN E:200 , ASN E:202 , PHE E:204 , TPW E:1370
BINDING SITE FOR RESIDUE MG E 369
08
AC8
SOFTWARE
HOH E:1466 , HOH F:1358 , HOH G:1410 , HOH H:1480 , HOH H:1481
BINDING SITE FOR RESIDUE MG E 370
09
AC9
SOFTWARE
TYR A:102 , ARG A:103 , ILE A:142 , ILE A:144 , GLY A:172 , ASP A:173 , GLY A:174 , GLY A:175 , GLN A:178 , ASN A:202 , PHE A:204 , ALA A:205 , ARG A:267 , HIS A:271 , MG A:1368 , HOH A:1410 , HOH A:1412 , HOH A:1463 , HOH A:1482 , HOH A:1493 , GLU D:28 , LEU D:57 , GLU D:59 , GLN D:81 , PHE D:85
BINDING SITE FOR RESIDUE TPW A1370
10
BC1
SOFTWARE
GLU B:28 , LEU B:57 , GLU B:59 , GLN B:81 , PHE B:85 , TYR C:102 , ARG C:103 , ILE C:142 , ILE C:144 , GLY C:172 , ASP C:173 , GLY C:174 , GLY C:175 , GLN C:178 , ASN C:202 , PHE C:204 , ALA C:205 , ALA C:206 , HIS C:271 , MG C:1368 , HOH C:1382 , HOH C:1394 , HOH C:1413 , HOH C:1432 , HOH C:1444 , HOH C:1455
BINDING SITE FOR RESIDUE TPW C1370
11
BC2
SOFTWARE
TYR E:102 , ARG E:103 , ILE E:142 , ILE E:144 , GLY E:172 , ASP E:173 , GLY E:174 , GLY E:175 , GLN E:178 , ASN E:202 , PHE E:204 , ALA E:205 , ALA E:206 , HIS E:271 , MG E:369 , HOH E:1458 , HOH E:1478 , HOH E:1496 , GLU H:28 , LEU H:57 , GLU H:59 , GLN H:81 , PHE H:85
BINDING SITE FOR RESIDUE TPW E1370
12
BC3
SOFTWARE
GLU F:28 , LEU F:57 , GLU F:59 , GLN F:81 , PHE F:85 , TYR G:102 , ARG G:103 , ILE G:142 , ILE G:144 , GLY G:172 , ASP G:173 , GLY G:174 , GLY G:175 , GLN G:178 , ASN G:202 , PHE G:204 , ALA G:205 , ALA G:206 , HIS G:271 , MG G:369 , HOH G:1407 , HOH G:1408 , HOH G:1411 , HOH G:1459 , HOH G:1461
BINDING SITE FOR RESIDUE TPW G1370
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: PSBD (I:130-167,J:130-167)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PSBD
PS51826
Peripheral subunit-binding (PSBD) domain profile.
ODP2_GEOSE
130-167
2
I:130-167
J:130-167
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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
(4, 14)
Info
All SCOP Domains
1a: SCOP_d3dvai_ (I:)
1b: SCOP_d3dvaj_ (J:)
2a: SCOP_d3dvab1 (B:1-186)
2b: SCOP_d3dvad1 (D:1-186)
2c: SCOP_d3dvaf1 (F:1-186)
2d: SCOP_d3dvah1 (H:1-186)
3a: SCOP_d3dvaa_ (A:)
3b: SCOP_d3dvac_ (C:)
3c: SCOP_d3dvae_ (E:)
3d: SCOP_d3dvag_ (G:)
4a: SCOP_d3dvab2 (B:187-324)
4b: SCOP_d3dvad2 (D:187-324)
4c: SCOP_d3dvaf2 (F:187-324)
4d: SCOP_d3dvah2 (H:187-324)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
(21)
Superfamily
:
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
(21)
Family
:
automated matches
(5)
Protein domain
:
automated matches
(5)
Bacillus stearothermophilus [TaxId: 1422]
(3)
1a
d3dvai_
I:
1b
d3dvaj_
J:
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Superfamily
:
Thiamin diphosphate-binding fold (THDP-binding)
(289)
Family
:
automated matches
(65)
Protein domain
:
automated matches
(65)
Bacillus stearothermophilus [TaxId: 1422]
(3)
2a
d3dvab1
B:1-186
2b
d3dvad1
D:1-186
2c
d3dvaf1
F:1-186
2d
d3dvah1
H:1-186
Family
:
Branched-chain alpha-keto acid dehydrogenase PP module
(42)
Protein domain
:
automated matches
(9)
Bacillus stearothermophilus [TaxId: 1422]
(3)
3a
d3dvaa_
A:
3b
d3dvac_
C:
3c
d3dvae_
E:
3d
d3dvag_
G:
Fold
:
TK C-terminal domain-like
(79)
Superfamily
:
TK C-terminal domain-like
(79)
Family
:
automated matches
(9)
Protein domain
:
automated matches
(9)
Bacillus stearothermophilus [TaxId: 1422]
(3)
4a
d3dvab2
B:187-324
4b
d3dvad2
D:187-324
4c
d3dvaf2
F:187-324
4d
d3dvah2
H:187-324
[
close SCOP info
]
CATH Domains
(3, 13)
Info
all CATH domains
1a: CATH_3dvaB02 (B:192-324)
1b: CATH_3dvaD02 (D:192-324)
1c: CATH_3dvaF02 (F:192-324)
1d: CATH_3dvaH02 (H:192-324)
2a: CATH_3dvaB01 (B:1-191)
2b: CATH_3dvaD01 (D:1-191)
2c: CATH_3dvaF01 (F:1-191)
2d: CATH_3dvaE00 (E:4-368)
2e: CATH_3dvaA00 (A:4-368)
2f: CATH_3dvaC00 (C:4-368)
2g: CATH_3dvaG00 (G:4-368)
2h: CATH_3dvaH01 (H:1-191)
3a: CATH_3dvaI00 (I:128-169)
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Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.920, no name defined]
(73)
Bacillus stearothermophilus.
(3)
1a
3dvaB02
B:192-324
1b
3dvaD02
D:192-324
1c
3dvaF02
F:192-324
1d
3dvaH02
H:192-324
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Bacillus stearothermophilus.
(3)
2a
3dvaB01
B:1-191
2b
3dvaD01
D:1-191
2c
3dvaF01
F:1-191
2d
3dvaE00
E:4-368
2e
3dvaA00
A:4-368
2f
3dvaC00
C:4-368
2g
3dvaG00
G:4-368
2h
3dvaH01
H:1-191
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Dihydrolipoamide Transferase
(20)
Homologous Superfamily
:
Dihydrolipoamide Transferase
(20)
Bacillus stearothermophilus.
(2)
3a
3dvaI00
I:128-169
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Atom Selection
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Chain J
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Asym.Unit (888 KB)
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