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2BFB
Biol. Unit 1
Info
Asym.Unit (141 KB)
Biol.Unit 1 (261 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
:
06 Dec 04 (Deposition) - 16 Feb 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.77
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Oxidoreductase, Multi-Enzyme Complex, Acylation, Oxidative Decarboxylation, Maple Syrup Urine Disease, Thiamine Diphosphate, Phosphorylation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Machius, R. M. Wynn, J. L. Chuang, 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
(3, 6)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
2a: GLYCEROL (GOLa)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
4a: MANGANESE (II) ION (MNa)
5a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
6a: THIAMIN DIPHOSPHATE (TDPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
GOL
2
Ligand/Ion
GLYCEROL
3
K
-1
Ligand/Ion
POTASSIUM ION
4
MN
-1
Ligand/Ion
MANGANESE (II) ION
5
MRD
2
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
6
TDP
2
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
SER A:161 , PRO A:163 , THR A:166 , GLN A:167 , HOH A:2132 , HOH A:2198
BINDING SITE FOR RESIDUE K A1401
2
AC2
SOFTWARE
GLU A:193 , ASN A:222 , TYR A:224 , TDP A:1404 , HOH A:2360
BINDING SITE FOR RESIDUE MN A1402
3
AC3
SOFTWARE
ALA A:112 , LEU A:164 , ALA A:165 , GLN A:167 , ALA A:195 , HOH A:2211
BINDING SITE FOR RESIDUE CL A1403
4
AC4
SOFTWARE
TYR A:113 , HOH A:2195
BINDING SITE FOR RESIDUE CL A1505
5
AC5
SOFTWARE
GLY B:128 , LEU B:130 , THR B:131 , CYS B:178 , ASP B:181 , ASN B:183 , HOH B:2135
BINDING SITE FOR RESIDUE K B1343
6
AC6
SOFTWARE
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 , MN A:1402 , HOH A:2120 , HOH A:2211 , HOH A:2275 , HOH A:2360 , HOH A:2361 , GLU B:46 , LEU B:74 , GLU B:76 , GLN B:98 , TYR B:102
BINDING SITE FOR RESIDUE TDP A1404
7
AC7
SOFTWARE
ILE A:73 , GLU A:76 , GLN A:80 , ARG A:82 , VAL B:58 , HOH B:2060
BINDING SITE FOR RESIDUE MRD B1345
8
AC8
SOFTWARE
GLN A:374 , TRP B:260 , THR B:284 , GLU B:290 , THR B:294 , ARG B:309 , HOH B:2283
BINDING SITE FOR RESIDUE GOL B1344
[
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]
SAPs(SNPs)/Variants
(16, 32)
Info
(mutated residues are only available for the asymmetric unit)
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_015102 (F364C, chain A, )
15: VAR_004972 (Y368C, chain A, )
16: 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_015102
F
409
C
ODBA_HUMAN
Disease (MSUD1A)
---
A
F
364
C
15
UniProt
VAR_004972
Y
413
C
ODBA_HUMAN
Disease (MSUD1A)
---
A
Y
368
C
16
UniProt
VAR_004973
Y
438
N
ODBA_HUMAN
Disease (MSUD1A)
---
A
Y
393
N
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
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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, 3)
Info
All SCOP Domains
1a: SCOP_d2bfba1 (A:6-400)
2a: SCOP_d2bfbb1 (B:14-204)
3a: SCOP_d2bfbb2 (B:205-342)
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(
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(
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Folds
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(
)
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
:
Branched-chain alpha-keto acid dehydrogenase, PP module
(23)
Human (Homo sapiens) [TaxId: 9606]
(19)
1a
d2bfba1
A:6-400
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
d2bfbb1
B:14-204
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
d2bfbb2
B:205-342
[
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]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_2bfbB02 (B:214-338)
2a: CATH_2bfbB01 (B:17-213)
2b: CATH_2bfbA00 (A:6-400)
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)
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
2bfbB02
B:214-338
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Human (Homo sapiens)
(31)
2a
2bfbB01
B:17-213
2b
2bfbA00
A:6-400
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
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Label:
Sorry, no Info available
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