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3EXG
Biol. Unit 4
Info
Asym.Unit (1.6 MB)
Biol.Unit 1 (224 KB)
Biol.Unit 2 (223 KB)
Biol.Unit 3 (224 KB)
Biol.Unit 4 (222 KB)
Biol.Unit 5 (223 KB)
Biol.Unit 6 (225 KB)
Biol.Unit 7 (223 KB)
Biol.Unit 8 (224 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
:
3.01
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T,U,V,W,X,Y,Z,1,2,3,4,5,6
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Biol. Unit 4: M,N,O,P (1x)
Biol. Unit 5: Q,R,S,T (1x)
Biol. Unit 6: U,V,W,X (1x)
Biol. Unit 7: Y,Z,1,2 (1x)
Biol. Unit 8: 3,4,5,6 (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
(0, 0)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
1e: POTASSIUM ION (Ke)
1f: POTASSIUM ION (Kf)
1g: POTASSIUM ION (Kg)
1h: POTASSIUM ION (Kh)
1i: POTASSIUM ION (Ki)
1j: POTASSIUM ION (Kj)
1k: POTASSIUM ION (Kk)
1l: POTASSIUM ION (Kl)
1m: POTASSIUM ION (Km)
1n: POTASSIUM ION (Kn)
1o: POTASSIUM ION (Ko)
1p: POTASSIUM ION (Kp)
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Sites
(2, 2)
Info
All Sites
1: AC9 (SOFTWARE)
2: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC9
SOFTWARE
PRO N:111 , ILE N:112 , VAL N:113 , ALA N:160 , ILE N:161 , ASP N:163
BINDING SITE FOR RESIDUE K N1009
2
BC3
SOFTWARE
ALA P:160 , ILE P:161 , ASP P:163
BINDING SITE FOR RESIDUE K P1012
[
close Site info
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SAPs(SNPs)/Variants
(23, 43)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_004967 (L1V, chain N/P, )
02: VAR_004949 (R43C, chain M/O, )
03: VAR_004950 (H84D, chain M/O, )
04: VAR_030954 (Y102C, chain N/P, )
05: VAR_069381 (A107T, chain M/O, )
06: VAR_004951 (G133R, chain M/O, )
07: VAR_004952 (V138M, chain M/O, )
08: VAR_004953 (A170T, chain M/O, )
09: VAR_004954 (F176L, chain M/O, )
10: VAR_004955 (M181V, chain M/O, )
11: VAR_004956 (P188L, chain M/O, )
12: VAR_021053 (Y214N, chain M/O, )
13: VAR_004958 (D229A, chain M/O, )
14: VAR_004959 (R234G, chain M/O, )
15: VAR_004960 (R234Q, chain M/O, )
16: VAR_021054 (M253L, chain M/O, )
17: VAR_021055 (R259H, chain M, )
18: VAR_004962 (R273C, chain M, )
19: VAR_004963 (R273H, chain M, )
20: VAR_021056 (D286N, chain M/O, )
21: VAR_050436 (E304D, chain M/O, )
22: VAR_021058 (P314S, chain N/P, )
23: VAR_004966 (R349H, chain M/O, )
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
---
N/P
L
1
V
02
UniProt
VAR_004949
R
72
C
ODPA_HUMAN
Disease (PDHAD)
---
M/O
R
43
C
03
UniProt
VAR_004950
H
113
D
ODPA_HUMAN
Disease (PDHAD)
---
M/O
H
84
D
04
UniProt
VAR_030954
Y
132
C
ODPB_HUMAN
Disease (PDHBD)
28935769
N/P
Y
102
C
05
UniProt
VAR_069381
A
136
T
ODPA_HUMAN
Disease
---
M/O
A
107
T
06
UniProt
VAR_004951
G
162
R
ODPA_HUMAN
Disease (PDHAD)
---
M/O
G
133
R
07
UniProt
VAR_004952
V
167
M
ODPA_HUMAN
Disease (PDHAD)
---
M/O
V
138
M
08
UniProt
VAR_004953
A
199
T
ODPA_HUMAN
Disease (PDHAD)
---
M/O
A
170
T
09
UniProt
VAR_004954
F
205
L
ODPA_HUMAN
Disease (PDHAD)
---
M/O
F
176
L
10
UniProt
VAR_004955
M
210
V
ODPA_HUMAN
Disease (PDHAD)
---
M/O
M
181
V
11
UniProt
VAR_004956
P
217
L
ODPA_HUMAN
Disease (PDHAD)
---
M/O
P
188
L
12
UniProt
VAR_021053
Y
243
N
ODPA_HUMAN
Disease (PDHAD)
---
M/O
Y
214
N
13
UniProt
VAR_004958
D
258
A
ODPA_HUMAN
Disease (PDHAD)
---
M/O
D
229
A
14
UniProt
VAR_004959
R
263
G
ODPA_HUMAN
Disease (PDHAD)
28936081
M/O
R
234
G
15
UniProt
VAR_004960
R
263
Q
ODPA_HUMAN
Disease (PDHAD)
---
M/O
R
234
Q
16
UniProt
VAR_021054
M
282
L
ODPA_HUMAN
Polymorphism
2229137
M/O
M
253
L
17
UniProt
VAR_021055
R
288
H
ODPA_HUMAN
Disease (PDHAD)
---
M
R
259
H
18
UniProt
VAR_004962
R
302
C
ODPA_HUMAN
Disease (PDHAD)
---
M
R
273
C
19
UniProt
VAR_004963
R
302
H
ODPA_HUMAN
Disease (PDHAD)
---
M
R
273
H
20
UniProt
VAR_021056
D
315
N
ODPA_HUMAN
Disease (PDHAD)
28935187
M/O
D
286
N
21
UniProt
VAR_050436
E
333
D
ODPA_HUMAN
Polymorphism
2228067
M/O
E
304
D
22
UniProt
VAR_021058
P
344
S
ODPB_HUMAN
Disease (PDHBD)
28933391
N/P
P
314
S
23
UniProt
VAR_004966
R
378
H
ODPA_HUMAN
Disease (PDHAD)
---
M/O
R
349
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
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, 48)
Info
All SCOP Domains
1a: SCOP_d3exg1_ (1:)
1b: SCOP_d3exg3_ (3:)
1c: SCOP_d3exg5_ (5:)
1d: SCOP_d3exga_ (A:)
1e: SCOP_d3exgc_ (C:)
1f: SCOP_d3exge_ (E:)
1g: SCOP_d3exgg_ (G:)
1h: SCOP_d3exgi_ (I:)
1i: SCOP_d3exgk_ (K:)
1j: SCOP_d3exgm_ (M:)
1k: SCOP_d3exgo_ (O:)
1l: SCOP_d3exgq_ (Q:)
1m: SCOP_d3exgs_ (S:)
1n: SCOP_d3exgu_ (U:)
1o: SCOP_d3exgw_ (W:)
1p: SCOP_d3exgy_ (Y:)
2a: SCOP_d3exg21 (2:1-191)
2b: SCOP_d3exg61 (6:1-191)
2c: SCOP_d3exgb1 (B:1-191)
2d: SCOP_d3exgd1 (D:1-191)
2e: SCOP_d3exgf1 (F:1-191)
2f: SCOP_d3exgh1 (H:1-191)
2g: SCOP_d3exgj1 (J:1-191)
2h: SCOP_d3exgl1 (L:1-191)
2i: SCOP_d3exgn1 (N:1-191)
2j: SCOP_d3exgp1 (P:1-191)
2k: SCOP_d3exgr1 (R:1-191)
2l: SCOP_d3exgt1 (T:1-191)
2m: SCOP_d3exgv1 (V:1-191)
2n: SCOP_d3exgx1 (X:1-191)
2o: SCOP_d3exgz1 (Z:1-191)
2p: SCOP_d3exg41 (4:1-191)
3a: SCOP_d3exg22 (2:192-329)
3b: SCOP_d3exg42 (4:192-329)
3c: SCOP_d3exg62 (6:192-329)
3d: SCOP_d3exgb2 (B:192-329)
3e: SCOP_d3exgd2 (D:192-329)
3f: SCOP_d3exgf2 (F:192-329)
3g: SCOP_d3exgh2 (H:192-329)
3h: SCOP_d3exgj2 (J:192-329)
3i: SCOP_d3exgl2 (L:192-329)
3j: SCOP_d3exgn2 (N:192-329)
3k: SCOP_d3exgp2 (P:192-329)
3l: SCOP_d3exgr2 (R:192-329)
3m: SCOP_d3exgt2 (T:192-329)
3n: SCOP_d3exgv2 (V:192-329)
3o: SCOP_d3exgx2 (X:192-329)
3p: SCOP_d3exgz2 (Z:192-329)
View:
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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
d3exg1_
1:
1b
d3exg3_
3:
1c
d3exg5_
5:
1d
d3exga_
A:
1e
d3exgc_
C:
1f
d3exge_
E:
1g
d3exgg_
G:
1h
d3exgi_
I:
1i
d3exgk_
K:
1j
d3exgm_
M:
1k
d3exgo_
O:
1l
d3exgq_
Q:
1m
d3exgs_
S:
1n
d3exgu_
U:
1o
d3exgw_
W:
1p
d3exgy_
Y:
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
d3exg21
2:1-191
2b
d3exg61
6:1-191
2c
d3exgb1
B:1-191
2d
d3exgd1
D:1-191
2e
d3exgf1
F:1-191
2f
d3exgh1
H:1-191
2g
d3exgj1
J:1-191
2h
d3exgl1
L:1-191
2i
d3exgn1
N:1-191
2j
d3exgp1
P:1-191
2k
d3exgr1
R:1-191
2l
d3exgt1
T:1-191
2m
d3exgv1
V:1-191
2n
d3exgx1
X:1-191
2o
d3exgz1
Z:1-191
2p
d3exg41
4:1-191
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
d3exg22
2:192-329
3b
d3exg42
4:192-329
3c
d3exg62
6:192-329
3d
d3exgb2
B:192-329
3e
d3exgd2
D:192-329
3f
d3exgf2
F:192-329
3g
d3exgh2
H:192-329
3h
d3exgj2
J:192-329
3i
d3exgl2
L:192-329
3j
d3exgn2
N:192-329
3k
d3exgp2
P:192-329
3l
d3exgr2
R:192-329
3m
d3exgt2
T:192-329
3n
d3exgv2
V:192-329
3o
d3exgx2
X:192-329
3p
d3exgz2
Z:192-329
[
close SCOP info
]
CATH Domains
(2, 33)
Info
all CATH domains
1a: CATH_3exg202 (2:195-328)
1b: CATH_3exg402 (4:195-328)
1c: CATH_3exg602 (6:195-328)
1d: CATH_3exgB02 (B:195-328)
1e: CATH_3exgD02 (D:195-328)
1f: CATH_3exgF02 (F:195-328)
1g: CATH_3exgH02 (H:195-328)
1h: CATH_3exgJ02 (J:195-328)
1i: CATH_3exgL02 (L:195-328)
1j: CATH_3exgN02 (N:195-328)
1k: CATH_3exgP02 (P:195-328)
1l: CATH_3exgR02 (R:195-328)
1m: CATH_3exgT02 (T:195-328)
1n: CATH_3exgV02 (V:195-328)
1o: CATH_3exgX02 (X:195-328)
1p: CATH_3exgZ02 (Z:195-328)
2a: CATH_3exg201 (2:2-194)
2b: CATH_3exg401 (4:2-194)
2c: CATH_3exg601 (6:2-194)
2d: CATH_3exgB01 (B:2-194)
2e: CATH_3exgD01 (D:2-194)
2f: CATH_3exgF01 (F:2-194)
2g: CATH_3exgH01 (H:2-194)
2h: CATH_3exgJ01 (J:2-194)
2i: CATH_3exgL01 (L:2-194)
2j: CATH_3exgN01 (N:2-194)
2k: CATH_3exgP01 (P:2-194)
2l: CATH_3exgR01 (R:2-194)
2m: CATH_3exgT01 (T:2-194)
2n: CATH_3exgV01 (V:2-194)
2o: CATH_3exgX01 (X:2-194)
2p: CATH_3exgZ01 (Z:2-194)
2q: CATH_3exgA00 (A:0-361)
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)
(
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(
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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)
Human (Homo sapiens)
(31)
1a
3exg202
2:195-328
1b
3exg402
4:195-328
1c
3exg602
6:195-328
1d
3exgB02
B:195-328
1e
3exgD02
D:195-328
1f
3exgF02
F:195-328
1g
3exgH02
H:195-328
1h
3exgJ02
J:195-328
1i
3exgL02
L:195-328
1j
3exgN02
N:195-328
1k
3exgP02
P:195-328
1l
3exgR02
R:195-328
1m
3exgT02
T:195-328
1n
3exgV02
V:195-328
1o
3exgX02
X:195-328
1p
3exgZ02
Z:195-328
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Human (Homo sapiens)
(31)
2a
3exg201
2:2-194
2b
3exg401
4:2-194
2c
3exg601
6:2-194
2d
3exgB01
B:2-194
2e
3exgD01
D:2-194
2f
3exgF01
F:2-194
2g
3exgH01
H:2-194
2h
3exgJ01
J:2-194
2i
3exgL01
L:2-194
2j
3exgN01
N:2-194
2k
3exgP01
P:2-194
2l
3exgR01
R:2-194
2m
3exgT01
T:2-194
2n
3exgV01
V:2-194
2o
3exgX01
X:2-194
2p
3exgZ01
Z:2-194
2q
3exgA00
A:0-361
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Pfam Domains
(0, 0)
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all PFAM domains
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