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3DV0
Biol. Unit 1
Info
Asym.Unit (469 KB)
Biol.Unit 1 (236 KB)
Biol.Unit 2 (230 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
:
2.50
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)
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)
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
(2, 4)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
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: PYRUVIC ACID (PYRa)
3b: PYRUVIC ACID (PYRb)
4a: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPWa)
4b: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPWb)
4c: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPWc)
4d: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (TPWd)
View:
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Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
PYR
2
Ligand/Ion
PYRUVIC ACID
4
TPW
2
Ligand/Ion
2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-METHYLTHIOPHEN-2-YL}ETHYL TRIHYDROGEN DIPHOSPHATE
[
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Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
9: AC9 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:173 , ASN A:202 , PHE A:204 , TPW A:1370
BINDING SITE FOR RESIDUE MG A1368
2
AC2
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 , ILE A:206 , ARG A:267 , MG A:1368 , HOH A:1489 , GLU D:28 , LEU D:57 , GLU D:59 , GLN D:81 , PHE D:85 , PYR D:502
BINDING SITE FOR RESIDUE TPW A1370
3
AC3
SOFTWARE
ILE B:112 , THR B:113 , ALA B:160 , ASP B:163 , ASP B:165 , HOH B:1344
BINDING SITE FOR RESIDUE K B1325
4
AC4
SOFTWARE
GLU A:183 , HOH A:1375 , HOH A:1436 , GLU B:88 , HOH B:1436 , HOH C:1421 , HOH D:1439
BINDING SITE FOR RESIDUE MG B1326
5
AC5
SOFTWARE
PHE B:82 , HIS B:128 , HOH B:1379 , PHE C:74 , ILE C:142 , TPW C:1370 , HOH C:1401
BINDING SITE FOR RESIDUE PYR B 502
6
AC6
SOFTWARE
ASP C:173 , ASN C:202 , PHE C:204 , TPW C:1370
BINDING SITE FOR RESIDUE MG C1368
7
AC7
SOFTWARE
GLU B:28 , LEU B:57 , GLU B:59 , GLN B:81 , PHE B:85 , PYR B:502 , 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 , ILE C:206 , HIS C:271 , MG C:1368 , HOH C:1442
BINDING SITE FOR RESIDUE TPW C1370
8
AC8
SOFTWARE
ILE D:112 , THR D:113 , ALA D:160 , ASP D:163 , ASP D:165 , HOH D:1328
BINDING SITE FOR RESIDUE K D1325
9
AC9
SOFTWARE
ILE A:142 , TPW A:1370 , GLN D:81 , PHE D:82 , PHE D:85 , HIS D:128
BINDING SITE FOR RESIDUE PYR D 502
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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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PSBD (I:130-167)
;
View:
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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
1
I:130-167
-
[
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 14)
Info
All SCOP Domains
1a: SCOP_d3dv0i_ (I:)
1b: SCOP_d3dv0j_ (J:)
2a: SCOP_d3dv0b1 (B:1-186)
2b: SCOP_d3dv0d1 (D:1-186)
2c: SCOP_d3dv0f1 (F:1-186)
2d: SCOP_d3dv0h1 (H:1-186)
3a: SCOP_d3dv0a_ (A:)
3b: SCOP_d3dv0c_ (C:)
3c: SCOP_d3dv0e_ (E:)
3d: SCOP_d3dv0g_ (G:)
4a: SCOP_d3dv0b2 (B:187-324)
4b: SCOP_d3dv0d2 (D:187-324)
4c: SCOP_d3dv0f2 (F:187-324)
4d: SCOP_d3dv0h2 (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
d3dv0i_
I:
1b
d3dv0j_
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
d3dv0b1
B:1-186
2b
d3dv0d1
D:1-186
2c
d3dv0f1
F:1-186
2d
d3dv0h1
H:1-186
Family
:
Branched-chain alpha-keto acid dehydrogenase PP module
(42)
Protein domain
:
automated matches
(9)
Bacillus stearothermophilus [TaxId: 1422]
(3)
3a
d3dv0a_
A:
3b
d3dv0c_
C:
3c
d3dv0e_
E:
3d
d3dv0g_
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
d3dv0b2
B:187-324
4b
d3dv0d2
D:187-324
4c
d3dv0f2
F:187-324
4d
d3dv0h2
H:187-324
[
close SCOP info
]
CATH Domains
(3, 13)
Info
all CATH domains
1a: CATH_3dv0B02 (B:192-324)
1b: CATH_3dv0F02 (F:192-324)
1c: CATH_3dv0H02 (H:192-324)
1d: CATH_3dv0D02 (D:192-324)
2a: CATH_3dv0B01 (B:1-191)
2b: CATH_3dv0F01 (F:1-191)
2c: CATH_3dv0H01 (H:1-191)
2d: CATH_3dv0E00 (E:4-367)
2e: CATH_3dv0A00 (A:4-367)
2f: CATH_3dv0C00 (C:4-368)
2g: CATH_3dv0G00 (G:4-367)
2h: CATH_3dv0D01 (D:1-191)
3a: CATH_3dv0I00 (I:127-169)
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)
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
3dv0B02
B:192-324
1b
3dv0F02
F:192-324
1c
3dv0H02
H:192-324
1d
3dv0D02
D:192-324
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Bacillus stearothermophilus.
(3)
2a
3dv0B01
B:1-191
2b
3dv0F01
F:1-191
2c
3dv0H01
H:1-191
2d
3dv0E00
E:4-367
2e
3dv0A00
A:4-367
2f
3dv0C00
C:4-368
2g
3dv0G00
G:4-367
2h
3dv0D01
D:1-191
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Dihydrolipoamide Transferase
(20)
Homologous Superfamily
:
Dihydrolipoamide Transferase
(20)
Bacillus stearothermophilus.
(2)
3a
3dv0I00
I:127-169
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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