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1W88
Asym. Unit
Info
Asym.Unit (451 KB)
Biol.Unit 1 (228 KB)
Biol.Unit 2 (220 KB)
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(1)
Title
:
THE CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE E1(D180N, E183Q) BOUND TO THE PERIPHERAL SUBUNIT BINDING DOMAIN OF E2
Authors
:
R. A. W. Frank, J. V. Pratap, X. Y. Pei, R. N. Perham, B. F. Luisi
Date
:
16 Sep 04 (Deposition) - 02 Nov 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
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
:
Pyruvate Dehydrogenase, Dihydrolipoyl, Acetyl Transferase, Multienzyme Complex, Oxidoreductase, Transferase, Catalysis, Slinky
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. A. W. Frank, C. M. Titman, J. V. Pratap, B. F. Luisi, R. N. Perham
A Molecular Switch And Proton-Wire Synchronize The Active Sites In Thiamine-Dependent Enzymes
Science V. 306 872 2004
(for further references see the
PDB file header
)
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Hetero Components
(2, 8)
Info
All Hetero Components
1a: MAGNESIUM ION (MGa)
1b: MAGNESIUM ION (MGb)
1c: MAGNESIUM ION (MGc)
1d: MAGNESIUM ION (MGd)
2a: THIAMIN DIPHOSPHATE (TDPa)
2b: THIAMIN DIPHOSPHATE (TDPb)
2c: THIAMIN DIPHOSPHATE (TDPc)
2d: THIAMIN DIPHOSPHATE (TDPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
MG
4
Ligand/Ion
MAGNESIUM ION
2
TDP
4
Ligand/Ion
THIAMIN DIPHOSPHATE
[
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Sites
(8, 8)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:173 , ASN A:202 , PHE A:204 , TDP A:1370
BINDING SITE FOR RESIDUE MG A1368
2
AC2
SOFTWARE
ASP C:173 , ASN C:202 , PHE C:204 , TDP C:1370 , HOH C:2095
BINDING SITE FOR RESIDUE MG C1368
3
AC3
SOFTWARE
ASP E:173 , GLN E:200 , ASN E:202 , TDP E:1370
BINDING SITE FOR RESIDUE MG E1368
4
AC4
SOFTWARE
ASP G:173 , ASN G:202 , TDP G:1370
BINDING SITE FOR RESIDUE MG G1368
5
AC5
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 , MG A:1368 , HOH A:2096 , GLU D:28 , LEU D:57 , GLU D:59 , GLN D:81 , PHE D:85
BINDING SITE FOR RESIDUE TDP A1370
6
AC6
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 , ILE C:206 , ARG C:267 , MG C:1368 , HOH C:2095 , HOH C:2167 , HOH C:2168
BINDING SITE FOR RESIDUE TDP C1370
7
AC7
SOFTWARE
TYR E:102 , ARG E:103 , ILE E:144 , GLY E:172 , ASP E:173 , GLY E:174 , GLY E:175 , ASN E:202 , MG E:1368 , GLU H:28 , GLU H:59 , PHE H:85
BINDING SITE FOR RESIDUE TDP E1370
8
AC8
SOFTWARE
GLU F:28 , TYR G:102 , ARG G:103 , ILE G:142 , ILE G:143 , ILE G:144 , GLY G:172 , ASP G:173 , GLY G:174 , GLY G:175 , ASN G:202 , MG G:1368
BINDING SITE FOR RESIDUE TDP G1370
[
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
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Label:
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
View:
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All Exon Boundaries
View:
Label:
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_d1w88i_ (I:)
1b: SCOP_d1w88j_ (J:)
2a: SCOP_d1w88a_ (A:)
2b: SCOP_d1w88c_ (C:)
2c: SCOP_d1w88e_ (E:)
2d: SCOP_d1w88g_ (G:)
3a: SCOP_d1w88b1 (B:1-192)
3b: SCOP_d1w88d1 (D:1-192)
3c: SCOP_d1w88f1 (F:1-192)
3d: SCOP_d1w88h1 (H:1-192)
4a: SCOP_d1w88b2 (B:193-324)
4b: SCOP_d1w88d2 (D:193-324)
4c: SCOP_d1w88f2 (F:193-324)
4d: SCOP_d1w88h2 (H:193-324)
View:
Select:
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
:
Peripheral subunit-binding domain of 2-oxo acid dehydrogenase complex
(16)
Protein domain
:
E3/E1 binding domain of dihydrolipoyl acetyltransferase
(5)
Bacillus stearothermophilus [TaxId: 1422]
(5)
1a
d1w88i_
I:
1b
d1w88j_
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
:
Branched-chain alpha-keto acid dehydrogenase PP module
(42)
Protein domain
:
Pyruvate dehydrogenase E1-alpha, PdhA
(2)
Bacillus stearothermophilus [TaxId: 1422]
(2)
2a
d1w88a_
A:
2b
d1w88c_
C:
2c
d1w88e_
E:
2d
d1w88g_
G:
Family
:
Branched-chain alpha-keto acid dehydrogenase Pyr module
(36)
Protein domain
:
Pyruvate dehydrogenase E1-beta, PdhB, N-terminal domain
(2)
Bacillus stearothermophilus [TaxId: 1422]
(2)
3a
d1w88b1
B:1-192
3b
d1w88d1
D:1-192
3c
d1w88f1
F:1-192
3d
d1w88h1
H:1-192
Fold
:
TK C-terminal domain-like
(79)
Superfamily
:
TK C-terminal domain-like
(79)
Family
:
Branched-chain alpha-keto acid dehydrogenase beta-subunit, C-terminal-domain
(39)
Protein domain
:
Pyruvate dehydrogenase E1-beta, PdhB, C-terminal domain
(2)
Bacillus stearothermophilus [TaxId: 1422]
(2)
4a
d1w88b2
B:193-324
4b
d1w88d2
D:193-324
4c
d1w88f2
F:193-324
4d
d1w88h2
H:193-324
[
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]
CATH Domains
(3, 14)
Info
all CATH domains
1a: CATH_1w88B02 (B:192-324)
1b: CATH_1w88D02 (D:192-324)
1c: CATH_1w88F02 (F:192-324)
1d: CATH_1w88H02 (H:192-324)
2a: CATH_1w88B01 (B:1-191)
2b: CATH_1w88A00 (A:5-368)
2c: CATH_1w88C00 (C:5-368)
2d: CATH_1w88D01 (D:1-191)
2e: CATH_1w88H01 (H:1-191)
2f: CATH_1w88F01 (F:1-191)
2g: CATH_1w88E00 (E:5-368)
2h: CATH_1w88G00 (G:5-368)
3a: CATH_1w88J00 (J:128-170)
3b: CATH_1w88I00 (I:128-167)
View:
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Classes
(
)
(
)
Architectures
(
)
(
)
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)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(2)
1a
1w88B02
B:192-324
1b
1w88D02
D:192-324
1c
1w88F02
F:192-324
1d
1w88H02
H:192-324
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(2)
2a
1w88B01
B:1-191
2b
1w88A00
A:5-368
2c
1w88C00
C:5-368
2d
1w88D01
D:1-191
2e
1w88H01
H:1-191
2f
1w88F01
F:1-191
2g
1w88E00
E:5-368
2h
1w88G00
G:5-368
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Dihydrolipoamide Transferase
(20)
Homologous Superfamily
:
Dihydrolipoamide Transferase
(20)
Geobacillus stearothermophilus. Organism_taxid: 1422.
(4)
3a
1w88J00
J:128-170
3b
1w88I00
I:128-167
[
close CATH info
]
Pfam Domains
(4, 14)
Info
all PFAM domains
1a: PFAM_E1_dh_1w88G01 (G:50-341)
1b: PFAM_E1_dh_1w88G02 (G:50-341)
1c: PFAM_E1_dh_1w88G03 (G:50-341)
1d: PFAM_E1_dh_1w88G04 (G:50-341)
2a: PFAM_Transket_pyr_1w88H01 (H:1-179)
2b: PFAM_Transket_pyr_1w88H02 (H:1-179)
2c: PFAM_Transket_pyr_1w88H03 (H:1-179)
2d: PFAM_Transket_pyr_1w88H04 (H:1-179)
3a: PFAM_E3_binding_1w88J01 (J:128-165)
3b: PFAM_E3_binding_1w88J02 (J:128-165)
4a: PFAM_Transketolase_C_1w88H05 (H:193-315)
4b: PFAM_Transketolase_C_1w88H06 (H:193-315)
4c: PFAM_Transketolase_C_1w88H07 (H:193-315)
4d: PFAM_Transketolase_C_1w88H08 (H:193-315)
View:
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
THDP-binding
(106)
Family
:
E1_dh
(27)
Geobacillus stearothermophilus (Bacillus stearothermophilus)
(2)
1a
E1_dh-1w88G01
G:50-341
1b
E1_dh-1w88G02
G:50-341
1c
E1_dh-1w88G03
G:50-341
1d
E1_dh-1w88G04
G:50-341
Family
:
Transket_pyr
(45)
Geobacillus stearothermophilus (Bacillus stearothermophilus)
(2)
2a
Transket_pyr-1w88H01
H:1-179
2b
Transket_pyr-1w88H02
H:1-179
2c
Transket_pyr-1w88H03
H:1-179
2d
Transket_pyr-1w88H04
H:1-179
Clan
:
no clan defined [family: E3_binding]
(14)
Family
:
E3_binding
(14)
Geobacillus stearothermophilus (Bacillus stearothermophilus)
(7)
3a
E3_binding-1w88J01
J:128-165
3b
E3_binding-1w88J02
J:128-165
Clan
:
no clan defined [family: Transketolase_C]
(40)
Family
:
Transketolase_C
(40)
Geobacillus stearothermophilus (Bacillus stearothermophilus)
(2)
4a
Transketolase_C-1w88H05
H:193-315
4b
Transketolase_C-1w88H06
H:193-315
4c
Transketolase_C-1w88H07
H:193-315
4d
Transketolase_C-1w88H08
H:193-315
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