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2BEV
Asym. Unit
Info
Asym.Unit (145 KB)
Biol.Unit 1 (268 KB)
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(1)
Title
:
REACTIVITY MODULATION OF HUMAN BRANCHED-CHAIN ALPHA-KETOACID DEHYDROGENASE BY AN INTERNAL MOLECULAR SWITCH
Authors
:
M. Machius, R. M. Wynn, J. L. Chuang, D. R. Tomchick, C. A. Brautigam, D.
Date
:
30 Nov 04 (Deposition) - 16 Feb 06 (Release) - 21 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,B,C (2x)
Keywords
:
Oxidoreductase, Oxidative Decarboxylation, Maple Syrup Urine Disease, Thiamine Diphosphate, Phosphorylation, Conformational Switch
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Machius, R. M. Wynn, J. L. Chuang, J. Li, R. Kluger, D. Yu, D. R. Tomchick, C. A. Brautigam, D. T. Chuang
A Versatile Conformational Switch Regulates Reactivity In Human Branched-Chain Alpha-Ketoacid Dehydrogenase.
Structure V. 14 287 2006
(for further references see the
PDB file header
)
[
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Hetero Components
(5, 8)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
4a: MANGANESE (II) ION (MNa)
5a: C2-1-HYDROXY-2-METHYL-BUTYL-THIAMI... (THYa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
2
Ligand/Ion
CHLORIDE ION
2
GOL
2
Ligand/Ion
GLYCEROL
3
K
2
Ligand/Ion
POTASSIUM ION
4
MN
1
Ligand/Ion
MANGANESE (II) ION
5
THY
1
Ligand/Ion
C2-1-HYDROXY-2-METHYL-BUTYL-THIAMINDIPHOSPHATE
[
close Hetero Component info
]
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
SER A:161 , PRO A:163 , THR A:166 , GLN A:167 , HOH A:2130
BINDING SITE FOR RESIDUE K A1402
2
AC2
SOFTWARE
GLU A:193 , ASN A:222 , TYR A:224 , THY A:601 , HOH A:2381
BINDING SITE FOR RESIDUE MN A1403
3
AC3
SOFTWARE
HOH A:2367 , TRP B:330
BINDING SITE FOR RESIDUE CL A1404
4
AC4
SOFTWARE
PHE B:54
BINDING SITE FOR RESIDUE CL B1343
5
AC5
SOFTWARE
GLY B:128 , LEU B:130 , THR B:131 , CYS B:178 , ASP B:181 , ASN B:183 , HOH B:2175
BINDING SITE FOR RESIDUE K B1346
6
AC6
SOFTWARE
PHE A:85 , GLN A:112 , TYR A:113 , ARG A:114 , SER A:162 , LEU A:164 , GLY A:192 , GLU A:193 , GLY A:194 , ALA A:195 , GLU A:198 , ARG A:220 , ASN A:222 , TYR A:224 , ALA A:225 , ILE A:226 , HIS A:291 , MN A:1403 , HOH A:2272 , HOH A:2381 , GLU B:46 , LEU B:74 , GLU B:76 , GLN B:98 , TYR B:102 , HIS B:146
BINDING SITE FOR RESIDUE THY A 601
7
AC7
SOFTWARE
GLN A:374 , TRP B:260 , THR B:284 , GLU B:290 , THR B:294 , ARG B:309 , HOH B:2306
BINDING SITE FOR RESIDUE GOL B1344
8
AC8
SOFTWARE
ARG A:185 , VAL B:88 , PHE B:125 , HOH B:2101 , HOH B:2143 , HOH B:2307
BINDING SITE FOR RESIDUE GOL B1345
[
close Site info
]
SAPs(SNPs)/Variants
(17, 17)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_034361 (T106M, chain A, )
02: VAR_004968 (R114W, chain A, )
03: VAR_068348 (R120H, chain B, )
04: VAR_024851 (R133P, chain B, )
05: VAR_004969 (Q145K, chain A, )
06: VAR_004974 (H156R, chain B, )
07: VAR_069748 (T166M, chain A, )
08: VAR_069749 (A175V, chain A, )
09: VAR_004970 (A208T, chain A, )
10: VAR_024852 (G228S, chain B, )
11: VAR_015101 (G245R, chain A, )
12: VAR_004971 (I281T, chain A, )
13: VAR_068349 (Q296R, chain B, )
14: VAR_069750 (R301C, chain A, )
15: VAR_015102 (F364C, chain A, )
16: VAR_004972 (Y368C, chain A, )
17: VAR_004973 (Y393N, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_034361
T
151
M
ODBA_HUMAN
Polymorphism
34442879
A
T
106
M
02
UniProt
VAR_004968
R
159
W
ODBA_HUMAN
Disease (MSUD1A)
---
A
R
114
W
03
UniProt
VAR_068348
R
170
H
ODBB_HUMAN
Disease (MSUD1B)
---
B
R
120
H
04
UniProt
VAR_024851
R
183
P
ODBB_HUMAN
Disease (MSUD1B)
28934895
B
R
133
P
05
UniProt
VAR_004969
Q
190
K
ODBA_HUMAN
Disease (MSUD1A)
---
A
Q
145
K
06
UniProt
VAR_004974
H
206
R
ODBB_HUMAN
Disease (MSUD1B)
---
B
H
156
R
07
UniProt
VAR_069748
T
211
M
ODBA_HUMAN
Disease (MSUD1A)
---
A
T
166
M
08
UniProt
VAR_069749
A
220
V
ODBA_HUMAN
Disease (MSUD1A)
---
A
A
175
V
09
UniProt
VAR_004970
A
253
T
ODBA_HUMAN
Disease (MSUD1A)
---
A
A
208
T
10
UniProt
VAR_024852
G
278
S
ODBB_HUMAN
Disease (MSUD1B)
---
B
G
228
S
11
UniProt
VAR_015101
G
290
R
ODBA_HUMAN
Disease (MSUD1A)
---
A
G
245
R
12
UniProt
VAR_004971
I
326
T
ODBA_HUMAN
Disease (MSUD1A)
---
A
I
281
T
13
UniProt
VAR_068349
Q
346
R
ODBB_HUMAN
Disease (MSUD1B)
---
B
Q
296
R
14
UniProt
VAR_069750
R
346
C
ODBA_HUMAN
Disease (MSUD1A)
---
A
R
301
C
15
UniProt
VAR_015102
F
409
C
ODBA_HUMAN
Disease (MSUD1A)
---
A
F
364
C
16
UniProt
VAR_004972
Y
413
C
ODBA_HUMAN
Disease (MSUD1A)
---
A
Y
368
C
17
UniProt
VAR_004973
Y
438
N
ODBA_HUMAN
Disease (MSUD1A)
---
A
Y
393
N
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(18, 18)
Info
All Exons
Exon 1.2a (A:6-51)
Exon 1.3 (A:52-80)
Exon 1.4 (A:81-117)
Exon 1.5 (A:117-171)
Exon 1.6 (A:171-240)
Exon 1.7b (A:240-287)
Exon 1.8b (A:287-344 (gaps))
Exon 1.9b (A:345-400)
Exon 2.1 (B:2-16 (gaps))
Exon 2.3 (B:16-42)
Exon 2.4 (B:42-65)
Exon 2.6 (B:65-109)
Exon 2.7 (B:110-161)
Exon 2.9 (B:162-198)
Exon 2.10 (B:198-230)
Exon 2.11 (B:231-267)
Exon 2.13b (B:268-296)
Exon 2.14b (B:297-342)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.1a/1.2a
02: Boundary 1.2a/1.3
03: Boundary 1.3/1.4
04: Boundary 1.4/1.5
05: Boundary 1.5/1.6
06: Boundary 1.6/1.7b
07: Boundary 1.7b/1.8b
08: Boundary 1.8b/1.9b
09: Boundary 1.9b/-
10: Boundary -/2.1
11: Boundary 2.1/2.3
12: Boundary 2.3/2.4
13: Boundary 2.4/2.6
14: Boundary 2.6/2.7
15: Boundary 2.7/2.9
16: Boundary 2.9/2.10
17: Boundary 2.10/2.11
18: Boundary 2.11/2.13b
19: Boundary 2.13b/2.14b
20: Boundary 2.14b/2.14d
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
1.1a
ENST00000269980
1a
ENSE00001136590
chr19:
41903704-41903840
137
ODBA_HUMAN
1-36
36
0
-
-
1.2a
ENST00000269980
2a
ENSE00000951971
chr19:
41916542-41916721
180
ODBA_HUMAN
37-96
60
1
A:6-51
46
1.3
ENST00000269980
3
ENSE00001243623
chr19:
41916828-41916914
87
ODBA_HUMAN
97-125
29
1
A:52-80
29
1.4
ENST00000269980
4
ENSE00000951973
chr19:
41919954-41920062
109
ODBA_HUMAN
126-162
37
1
A:81-117
37
1.5
ENST00000269980
5
ENSE00001164733
chr19:
41925040-41925201
162
ODBA_HUMAN
162-216
55
1
A:117-171
55
1.6
ENST00000269980
6
ENSE00000951975
chr19:
41928069-41928275
207
ODBA_HUMAN
216-285
70
1
A:171-240
70
1.7b
ENST00000269980
7b
ENSE00000951976
chr19:
41928534-41928675
142
ODBA_HUMAN
285-332
48
1
A:240-287
48
1.8b
ENST00000269980
8b
ENSE00000951977
chr19:
41928903-41929074
172
ODBA_HUMAN
332-389
58
1
A:287-344 (gaps)
58
1.9b
ENST00000269980
9b
ENSE00001196086
chr19:
41930343-41930909
567
ODBA_HUMAN
390-445
56
1
A:345-400
56
2.1
ENST00000356489
1
ENSE00001140741
chr6:
80816364-80816606
243
ODBB_HUMAN
1-66
66
1
B:2-16 (gaps)
15
2.3
ENST00000356489
3
ENSE00002147378
chr6:
80837264-80837341
78
ODBB_HUMAN
66-92
27
1
B:16-42
27
2.4
ENST00000356489
4
ENSE00002146276
chr6:
80838878-80838946
69
ODBB_HUMAN
92-115
24
1
B:42-65
24
2.6
ENST00000356489
6
ENSE00000798033
chr6:
80877395-80877528
134
ODBB_HUMAN
115-159
45
1
B:65-109
45
2.7
ENST00000356489
7
ENSE00000798034
chr6:
80878592-80878747
156
ODBB_HUMAN
160-211
52
1
B:110-161
52
2.9
ENST00000356489
9
ENSE00000798035
chr6:
80880999-80881107
109
ODBB_HUMAN
212-248
37
1
B:162-198
37
2.10
ENST00000356489
10
ENSE00000798036
chr6:
80910651-80910748
98
ODBB_HUMAN
248-280
33
1
B:198-230
33
2.11
ENST00000356489
11
ENSE00002191509
chr6:
80912819-80912929
111
ODBB_HUMAN
281-317
37
1
B:231-267
37
2.13b
ENST00000356489
13b
ENSE00000759469
chr6:
80982852-80982938
87
ODBB_HUMAN
318-346
29
1
B:268-296
29
2.14b
ENST00000356489
14b
ENSE00001409003
chr6:
81053381-81053529
149
ODBB_HUMAN
347-392
46
1
B:297-342
46
2.14d
ENST00000356489
14d
ENSE00001417653
chr6:
81055692-81055971
280
ODBB_HUMAN
-
0
0
-
-
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d2beva_ (A:)
2a: SCOP_d2bevb1 (B:2-204)
3a: SCOP_d2bevb2 (B:205-342)
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Protein Domains
(
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(
)
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
:
automated matches
(9)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d2beva_
A:
Family
:
Branched-chain alpha-keto acid dehydrogenase Pyr module
(36)
Protein domain
:
Branched-chain alpha-keto acid dehydrogenase, Pyr module
(27)
Human (Homo sapiens) [TaxId: 9606]
(23)
2a
d2bevb1
B:2-204
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
:
Branched-chain alpha-keto acid dehydrogenase
(27)
Human (Homo sapiens) [TaxId: 9606]
(23)
3a
d2bevb2
B:205-342
[
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CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_2bevB02 (B:214-338)
2a: CATH_2bevB01 (B:17-213)
2b: CATH_2bevA00 (A:6-400)
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Homologous Superfamilies
(
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)
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
2bevB02
B:214-338
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Human (Homo sapiens)
(31)
2a
2bevB01
B:17-213
2b
2bevA00
A:6-400
[
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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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