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3EXI
Asym. Unit
Info
Asym.Unit (116 KB)
Biol.Unit 1 (216 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE PYRUVATE DEHYDROGENASE (E1P) COMPONENT OF HUMAN PYRUVATE DEHYDROGENASE COMPLEX WITH THE SUBUNIT-BINDING DOMAIN (SBD) OF E2P, BUT SBD CANNOT BE MODELED INTO THE ELECTRON DENSITY
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
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
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
(2, 3)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
1
Ligand/Ion
CHLORIDE ION
2
K
2
Ligand/Ion
POTASSIUM ION
[
close Hetero Component info
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Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA B:160 , ILE B:161 , ASP B:163 , HOH B:2023 , HOH B:2034
BINDING SITE FOR RESIDUE K A 1001
2
AC2
SOFTWARE
HOH A:2050 , HOH A:2201 , GLU B:173 , HOH B:2103 , HOH B:2166
BINDING SITE FOR RESIDUE K B 1002
3
AC3
SOFTWARE
ARG A:44 , ARG A:314 , ILE A:317
BINDING SITE FOR RESIDUE CL A 1003
[
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SAPs(SNPs)/Variants
(20, 20)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_004967 (L1V, chain B, )
02: VAR_004949 (R43C, chain A, )
03: VAR_004950 (H84D, chain A, )
04: VAR_030954 (Y102C, chain B, )
05: VAR_069381 (A107T, chain A, )
06: VAR_004951 (G133R, chain A, )
07: VAR_004952 (V138M, chain A, )
08: VAR_004953 (A170T, chain A, )
09: VAR_004954 (F176L, chain A, )
10: VAR_004955 (M181V, chain A, )
11: VAR_004956 (P188L, chain A, )
12: VAR_021053 (Y214N, chain A, )
13: VAR_004958 (D229A, chain A, )
14: VAR_004959 (R234G, chain A, )
15: VAR_004960 (R234Q, chain A, )
16: VAR_021054 (M253L, chain A, )
17: VAR_021056 (D286N, chain A, )
18: VAR_050436 (E304D, chain A, )
19: VAR_021058 (P314S, chain B, )
20: VAR_004966 (R349H, chain A, )
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
L
1
V
02
UniProt
VAR_004949
R
72
C
ODPA_HUMAN
Disease (PDHAD)
---
A
R
43
C
03
UniProt
VAR_004950
H
113
D
ODPA_HUMAN
Disease (PDHAD)
---
A
H
84
D
04
UniProt
VAR_030954
Y
132
C
ODPB_HUMAN
Disease (PDHBD)
28935769
B
Y
102
C
05
UniProt
VAR_069381
A
136
T
ODPA_HUMAN
Disease
---
A
A
107
T
06
UniProt
VAR_004951
G
162
R
ODPA_HUMAN
Disease (PDHAD)
---
A
G
133
R
07
UniProt
VAR_004952
V
167
M
ODPA_HUMAN
Disease (PDHAD)
---
A
V
138
M
08
UniProt
VAR_004953
A
199
T
ODPA_HUMAN
Disease (PDHAD)
---
A
A
170
T
09
UniProt
VAR_004954
F
205
L
ODPA_HUMAN
Disease (PDHAD)
---
A
F
176
L
10
UniProt
VAR_004955
M
210
V
ODPA_HUMAN
Disease (PDHAD)
---
A
M
181
V
11
UniProt
VAR_004956
P
217
L
ODPA_HUMAN
Disease (PDHAD)
---
A
P
188
L
12
UniProt
VAR_021053
Y
243
N
ODPA_HUMAN
Disease (PDHAD)
---
A
Y
214
N
13
UniProt
VAR_004958
D
258
A
ODPA_HUMAN
Disease (PDHAD)
---
A
D
229
A
14
UniProt
VAR_004959
R
263
G
ODPA_HUMAN
Disease (PDHAD)
28936081
A
R
234
G
15
UniProt
VAR_004960
R
263
Q
ODPA_HUMAN
Disease (PDHAD)
---
A
R
234
Q
16
UniProt
VAR_021054
M
282
L
ODPA_HUMAN
Polymorphism
2229137
A
M
253
L
17
UniProt
VAR_021056
D
315
N
ODPA_HUMAN
Disease (PDHAD)
28935187
A
D
286
N
18
UniProt
VAR_050436
E
333
D
ODPA_HUMAN
Polymorphism
2228067
A
E
304
D
19
UniProt
VAR_021058
P
344
S
ODPB_HUMAN
Disease (PDHBD)
28933391
B
P
314
S
20
UniProt
VAR_004966
R
378
H
ODPA_HUMAN
Disease (PDHAD)
---
A
R
349
H
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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Exons
(9, 9)
Info
All Exons
Exon 1.1j (B:1-2)
Exon 1.1l (B:3-38)
Exon 1.1n (B:39-59)
Exon 1.1q (B:60-71)
Exon 1.1t (B:72-167)
Exon 1.2b (B:167-204)
Exon 1.2e (B:204-234)
Exon 1.3a (B:235-282)
Exon 1.3h (B:282-329)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1b/1.1j
02: Boundary 1.1j/1.1l
03: Boundary 1.1l/1.1n
04: Boundary 1.1n/1.1q
05: Boundary 1.1q/1.1t
06: Boundary 1.1t/1.2b
07: Boundary 1.2b/1.2e
08: Boundary 1.2e/1.3a
09: Boundary 1.3a/1.3h
10: Boundary 1.3h/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000302746
1b
ENSE00001931564
chr3:
58419579-58419495
85
ODPB_HUMAN
1-14
14
0
-
-
1.1j
ENST00000302746
1j
ENSE00001168306
chr3:
58419411-58419358
54
ODPB_HUMAN
15-32
18
1
B:1-2
2
1.1l
ENST00000302746
1l
ENSE00001168363
chr3:
58417711-58417604
108
ODPB_HUMAN
33-68
36
1
B:3-38
36
1.1n
ENST00000302746
1n
ENSE00001168356
chr3:
58417520-58417458
63
ODPB_HUMAN
69-89
21
1
B:39-59
21
1.1q
ENST00000302746
1q
ENSE00001168351
chr3:
58417355-58417320
36
ODPB_HUMAN
90-101
12
1
B:60-71
12
1.1t
ENST00000302746
1t
ENSE00001168343
chr3:
58416669-58416384
286
ODPB_HUMAN
102-197
96
1
B:72-167
96
1.2b
ENST00000302746
2b
ENSE00001168337
chr3:
58415965-58415855
111
ODPB_HUMAN
197-234
38
1
B:167-204
38
1.2e
ENST00000302746
2e
ENSE00001168326
chr3:
58415526-58415435
92
ODPB_HUMAN
234-264
31
1
B:204-234
31
1.3a
ENST00000302746
3a
ENSE00001168314
chr3:
58414341-58414200
142
ODPB_HUMAN
265-312
48
1
B:235-282
48
1.3h
ENST00000302746
3h
ENSE00001835890
chr3:
58413906-58413357
550
ODPB_HUMAN
312-359
48
1
B:282-329
48
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d3exib1 (B:1-185)
2a: SCOP_d3exia_ (A:)
3a: SCOP_d3exib2 (B:186-329)
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
:
automated matches
(65)
Protein domain
:
automated matches
(65)
Human (Homo sapiens) [TaxId: 9606]
(4)
1a
d3exib1
B:1-185
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)
2a
d3exia_
A:
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
d3exib2
B:186-329
[
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_3exiB02 (B:195-328)
2a: CATH_3exiB01 (B:2-194)
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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
3exiB02
B:195-328
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Human (Homo sapiens)
(31)
2a
3exiB01
B: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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Asymmetric Unit 1
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