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3EXF
Biol. Unit 1
Info
Asym.Unit (435 KB)
Biol.Unit 1 (217 KB)
Biol.Unit 2 (217 KB)
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Title
:
CRYSTAL STRUCTURE OF THE PYRUVATE DEHYDROGENASE (E1P) COMPONENT OF HUMAN PYRUVATE DEHYDROGENASE COMPLEX
Authors
:
M. Kato, R. M. Wynn, J. L. Chuang, S. -C. Tso, M. Machius, J. Li, D. T. Chuan
Date
:
16 Oct 08 (Deposition) - 25 Nov 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Heterotetramer; Thiamine Diphosphate-Dependent Enzyme; Disease Mutation; Glycolysis; Leigh Syndrome; Mitochondrion; Oxidoreductase; Phosphoprotein; Alternative Splicing; Polymorphism; Pyruvate; Thiamine Pyrophosphate; Transit Peptide, Oxidoreductase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Kato, R. M. Wynn, J. L. Chuang, S. C. Tso, M. Machius, J. Li, D. T. Chuan
Structural Basis For Inactivation Of The Human Pyruvate Dehydrogenase Complex By Phosphorylation: Role Of Disordere Phosphorylation Loops.
Structure V. 16 1849 2008
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Hetero Components
(1, 2)
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)
3a: THIAMINE DIPHOSPHATE (TPPa)
3b: THIAMINE DIPHOSPHATE (TPPb)
3c: THIAMINE DIPHOSPHATE (TPPc)
3d: THIAMINE DIPHOSPHATE (TPPd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
MG
-1
Ligand/Ion
MAGNESIUM ION
3
TPP
2
Ligand/Ion
THIAMINE DIPHOSPHATE
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:167 , ASN A:196 , TYR A:198 , TPP A:1003
BINDING SITE FOR RESIDUE MG A1001
2
AC2
SOFTWARE
ARG D:75 , PRO D:111 , ALA D:160 , ILE D:161 , ASP D:163
BINDING SITE FOR RESIDUE K D1002
3
AC3
SOFTWARE
TYR A:89 , ARG A:90 , GLY A:136 , VAL A:138 , GLY A:166 , ASP A:167 , GLY A:168 , ALA A:169 , ASN A:196 , TYR A:198 , GLY A:199 , MET A:200 , HIS A:263 , MG A:1001 , GLU D:28 , ILE D:57 , GLU D:59 , PHE D:85 , GLN D:88
BINDING SITE FOR RESIDUE TPP A1003
4
AC4
SOFTWARE
ASP C:167 , ASN C:196 , TYR C:198 , TPP C:1006 , HOH C:2002
BINDING SITE FOR RESIDUE MG C1004
5
AC5
SOFTWARE
ILE B:112 , ALA B:160 , ILE B:161 , ASP B:163
BINDING SITE FOR RESIDUE K B1005
6
AC6
SOFTWARE
GLU B:28 , ILE B:57 , GLU B:59 , PHE B:85 , GLN B:88 , TYR C:89 , ARG C:90 , GLY C:136 , ILE C:137 , VAL C:138 , GLY C:166 , ASP C:167 , GLY C:168 , ALA C:169 , ASN C:196 , TYR C:198 , GLY C:199 , MET C:200 , MG C:1004 , HOH C:2002
BINDING SITE FOR RESIDUE TPP C1006
[
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]
SAPs(SNPs)/Variants
(25, 50)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_004967 (L1V, chain B/D, )
02: VAR_004949 (R43C, chain A/C, )
03: VAR_004950 (H84D, chain A/C, )
04: VAR_030954 (Y102C, chain B/D, )
05: VAR_069381 (A107T, chain A/C, )
06: VAR_004951 (G133R, chain A/C, )
07: VAR_004952 (V138M, chain A/C, )
08: VAR_004953 (A170T, chain A/C, )
09: VAR_004954 (F176L, chain A/C, )
10: VAR_004955 (M181V, chain A/C, )
11: VAR_004956 (P188L, chain A/C, )
12: VAR_004957 (T202A, chain A/C, )
13: VAR_021053 (Y214N, chain A/C, )
14: VAR_004958 (D229A, chain A/C, )
15: VAR_004959 (R234G, chain A/C, )
16: VAR_004960 (R234Q, chain A/C, )
17: VAR_021054 (M253L, chain A/C, )
18: VAR_021055 (R259H, chain A/C, )
19: VAR_004961 (H263L, chain A/C, )
20: VAR_004962 (R273C, chain A/C, )
21: VAR_004963 (R273H, chain A/C, )
22: VAR_021056 (D286N, chain A/C, )
23: VAR_050436 (E304D, chain A/C, )
24: VAR_021058 (P314S, chain B/D, )
25: VAR_004966 (R349H, chain A/C, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_004967
L
31
V
ODPB_HUMAN
Polymorphism
---
B/D
L
1
V
02
UniProt
VAR_004949
R
72
C
ODPA_HUMAN
Disease (PDHAD)
---
A/C
R
43
C
03
UniProt
VAR_004950
H
113
D
ODPA_HUMAN
Disease (PDHAD)
---
A/C
H
84
D
04
UniProt
VAR_030954
Y
132
C
ODPB_HUMAN
Disease (PDHBD)
28935769
B/D
Y
102
C
05
UniProt
VAR_069381
A
136
T
ODPA_HUMAN
Disease
---
A/C
A
107
T
06
UniProt
VAR_004951
G
162
R
ODPA_HUMAN
Disease (PDHAD)
---
A/C
G
133
R
07
UniProt
VAR_004952
V
167
M
ODPA_HUMAN
Disease (PDHAD)
---
A/C
V
138
M
08
UniProt
VAR_004953
A
199
T
ODPA_HUMAN
Disease (PDHAD)
---
A/C
A
170
T
09
UniProt
VAR_004954
F
205
L
ODPA_HUMAN
Disease (PDHAD)
---
A/C
F
176
L
10
UniProt
VAR_004955
M
210
V
ODPA_HUMAN
Disease (PDHAD)
---
A/C
M
181
V
11
UniProt
VAR_004956
P
217
L
ODPA_HUMAN
Disease (PDHAD)
---
A/C
P
188
L
12
UniProt
VAR_004957
T
231
A
ODPA_HUMAN
Disease (PDHAD)
---
A/C
T
202
A
13
UniProt
VAR_021053
Y
243
N
ODPA_HUMAN
Disease (PDHAD)
---
A/C
Y
214
N
14
UniProt
VAR_004958
D
258
A
ODPA_HUMAN
Disease (PDHAD)
---
A/C
D
229
A
15
UniProt
VAR_004959
R
263
G
ODPA_HUMAN
Disease (PDHAD)
28936081
A/C
R
234
G
16
UniProt
VAR_004960
R
263
Q
ODPA_HUMAN
Disease (PDHAD)
---
A/C
R
234
Q
17
UniProt
VAR_021054
M
282
L
ODPA_HUMAN
Polymorphism
2229137
A/C
M
253
L
18
UniProt
VAR_021055
R
288
H
ODPA_HUMAN
Disease (PDHAD)
---
A/C
R
259
H
19
UniProt
VAR_004961
H
292
L
ODPA_HUMAN
Disease (PDHAD)
---
A/C
H
263
L
20
UniProt
VAR_004962
R
302
C
ODPA_HUMAN
Disease (PDHAD)
---
A/C
R
273
C
21
UniProt
VAR_004963
R
302
H
ODPA_HUMAN
Disease (PDHAD)
---
A/C
R
273
H
22
UniProt
VAR_021056
D
315
N
ODPA_HUMAN
Disease (PDHAD)
28935187
A/C
D
286
N
23
UniProt
VAR_050436
E
333
D
ODPA_HUMAN
Polymorphism
2228067
A/C
E
304
D
24
UniProt
VAR_021058
P
344
S
ODPB_HUMAN
Disease (PDHBD)
28933391
B/D
P
314
S
25
UniProt
VAR_004966
R
378
H
ODPA_HUMAN
Disease (PDHAD)
---
A/C
R
349
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
[
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]
Exons
(0, 0)
Info
All Exons
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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.
(no "Exon" information available for biological units yet)
SCOP Domains
(3, 12)
Info
All SCOP Domains
1a: SCOP_d3exfa_ (A:)
1b: SCOP_d3exfc_ (C:)
1c: SCOP_d3exfe_ (E:)
1d: SCOP_d3exfg_ (G:)
2a: SCOP_d3exfb1 (B:1-191)
2b: SCOP_d3exfd1 (D:1-191)
2c: SCOP_d3exff1 (F:1-191)
2d: SCOP_d3exfh1 (H:1-191)
3a: SCOP_d3exfb2 (B:192-329)
3b: SCOP_d3exfd2 (D:192-329)
3c: SCOP_d3exff2 (F:192-329)
3d: SCOP_d3exfh2 (H:192-329)
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Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
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
:
E1-beta subunit of pyruvate dehydrogenase (PP module)
(7)
Human (Homo sapiens) [TaxId: 9606]
(7)
1a
d3exfa_
A:
1b
d3exfc_
C:
1c
d3exfe_
E:
1d
d3exfg_
G:
Family
:
Branched-chain alpha-keto acid dehydrogenase Pyr module
(36)
Protein domain
:
E1-beta subunit of pyruvate dehydrogenase, Pyr module
(5)
Human (Homo sapiens) [TaxId: 9606]
(4)
2a
d3exfb1
B:1-191
2b
d3exfd1
D:1-191
2c
d3exff1
F:1-191
2d
d3exfh1
H:1-191
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
:
E1-beta subunit of pyruvate dehydrogenase, C-domain
(8)
Human (Homo sapiens) [TaxId: 9606]
(7)
3a
d3exfb2
B:192-329
3b
d3exfd2
D:192-329
3c
d3exff2
F:192-329
3d
d3exfh2
H:192-329
[
close SCOP info
]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_3exfB02 (B:195-328)
1b: CATH_3exfD02 (D:195-328)
1c: CATH_3exfF02 (F:195-328)
1d: CATH_3exfH02 (H:195-328)
2a: CATH_3exfB01 (B:2-194)
2b: CATH_3exfD01 (D:2-194)
2c: CATH_3exfF01 (F:2-194)
2d: CATH_3exfH01 (H:2-194)
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(
)
(
)
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)
Human (Homo sapiens)
(31)
1a
3exfB02
B:195-328
1b
3exfD02
D:195-328
1c
3exfF02
F:195-328
1d
3exfH02
H:195-328
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Human (Homo sapiens)
(31)
2a
3exfB01
B:2-194
2b
3exfD01
D:2-194
2c
3exfF01
F:2-194
2d
3exfH01
H:2-194
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
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Label:
Sorry, no Info available
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Asym.Unit (435 KB)
Header - Asym.Unit
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Header - Biol.Unit 1
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