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3DUF
Biol. Unit 1
Info
Asym.Unit (466 KB)
Biol.Unit 1 (231 KB)
Biol.Unit 2 (231 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
:
17 Jul 08 (Deposition) - 06 Jan 09 (Release) - 06 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
(1, 2)
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)
3a: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (R1Ta)
3b: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (R1Tb)
3c: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (R1Tc)
3d: 2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5... (R1Td)
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
R1T
2
Ligand/Ion
2-{4-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-5-[(1R)-1-HYDROXYETHYL]-3-METHYL-2-THIENYL}ETHYL TRIHYDROGENDIPHOSPHATE
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:173 , ASN A:202 , PHE A:204 , R1T A:1370 , HOH A:1374
BINDING SITE FOR RESIDUE MG A1368
2
AC2
SOFTWARE
ILE B:112 , THR B:113 , ALA B:160 , ASP B:163 , ASP B:165
BINDING SITE FOR RESIDUE K B1325
3
AC3
SOFTWARE
HOH B:1344
BINDING SITE FOR RESIDUE MG D1326
4
AC4
SOFTWARE
ASP C:173 , ASN C:202 , PHE C:204 , R1T C:1370
BINDING SITE FOR RESIDUE MG C1368
5
AC5
SOFTWARE
ILE D:112 , THR D:113 , ALA D:160 , ASP D:163 , ASP D:165
BINDING SITE FOR RESIDUE K D1325
6
AC6
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 , HIS A:271 , MG A:1368 , HOH A:1374 , HOH A:1375 , HOH A:1393 , GLU D:28 , LEU D:57 , GLU D:59 , GLN D:81 , PHE D:85 , HIS D:128
BINDING SITE FOR RESIDUE R1T A1370
7
AC8
SOFTWARE
GLU B:28 , LEU B:57 , GLU B:59 , GLN B:81 , PHE B:85 , HIS B:128 , 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:1417
BINDING SITE FOR RESIDUE R1T C1370
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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:130-165)
;
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:130-165
-
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 14)
Info
All SCOP Domains
1a: SCOP_d3dufi_ (I:)
1b: SCOP_d3dufj_ (J:)
2a: SCOP_d3dufb1 (B:1-186)
2b: SCOP_d3duff1 (F:1-186)
2c: SCOP_d3dufh1 (H:1-186)
2d: SCOP_d3dufd1 (D:1-186)
3a: SCOP_d3dufa_ (A:)
3b: SCOP_d3dufe_ (E:)
3c: SCOP_d3dufg_ (G:)
3d: SCOP_d3dufc_ (C:)
4a: SCOP_d3dufb2 (B:187-324)
4b: SCOP_d3duff2 (F:187-324)
4c: SCOP_d3dufh2 (H:187-324)
4d: SCOP_d3dufd2 (D:187-324)
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)
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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
d3dufi_
I:
1b
d3dufj_
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
d3dufb1
B:1-186
2b
d3duff1
F:1-186
2c
d3dufh1
H:1-186
2d
d3dufd1
D:1-186
Family
:
Branched-chain alpha-keto acid dehydrogenase PP module
(42)
Protein domain
:
automated matches
(9)
Bacillus stearothermophilus [TaxId: 1422]
(3)
3a
d3dufa_
A:
3b
d3dufe_
E:
3c
d3dufg_
G:
3d
d3dufc_
C:
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
d3dufb2
B:187-324
4b
d3duff2
F:187-324
4c
d3dufh2
H:187-324
4d
d3dufd2
D:187-324
[
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CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_3dufB02 (B:192-324)
1b: CATH_3dufD02 (D:192-324)
1c: CATH_3dufF02 (F:192-324)
1d: CATH_3dufH02 (H:192-324)
2a: CATH_3dufB01 (B:1-191)
2b: CATH_3dufA00 (A:4-368)
2c: CATH_3dufC00 (C:4-368)
2d: CATH_3dufE00 (E:4-368)
2e: CATH_3dufG00 (G:4-368)
2f: CATH_3dufD01 (D:1-191)
2g: CATH_3dufF01 (F:1-191)
2h: CATH_3dufH01 (H:1-191)
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)
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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
3dufB02
B:192-324
1b
3dufD02
D:192-324
1c
3dufF02
F:192-324
1d
3dufH02
H:192-324
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Bacillus stearothermophilus.
(3)
2a
3dufB01
B:1-191
2b
3dufA00
A:4-368
2c
3dufC00
C:4-368
2d
3dufE00
E:4-368
2e
3dufG00
G:4-368
2f
3dufD01
D:1-191
2g
3dufF01
F:1-191
2h
3dufH01
H:1-191
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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