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1V16
Biol. Unit 1
Info
Asym.Unit (137 KB)
Biol.Unit 1 (253 KB)
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(1)
Title
:
CROSSTALK BETWEEN COFACTOR BINDING AND THE PHOSPHORYLATION LOOP CONFORMATION IN THE BCKD MACHINE
Authors
:
J. Li, R. M. Wynn, M. Machius, J. L. Chuang, S. Karthikeyan, D. R. Tomchic D. T. Chuang
Date
:
07 Apr 04 (Deposition) - 03 Jun 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Oxidoreductase, Ketoacid Dehydrogenase, Branched-Chain, Multi-Enzyme Complex, Acylation, Oxidative Decarboxylation Maple Syrup Urine Disease, Thiamine Diphosphate , Phosphorylation, Flavoprotein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Li, R. M. Wynn, M. Machius, J. L. Chuang, S. Karthikeyan, D. R. Tomchick, D. T. Chuang
Cross-Talk Between Thiamin Diphosphate Binding And Phosphorylation Loop Conformation In Human Branched-Chain {Alpha}-Keto Acid Decarboxylase/Dehydrogenase
J. Biol. Chem. V. 279 32968 2004
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 10)
Info
All Hetero Components
1a: BENZAMIDINE (BENa)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
4a: POTASSIUM ION (Ka)
4b: POTASSIUM ION (Kb)
5a: MANGANESE (II) ION (MNa)
6a: THIAMIN DIPHOSPHATE (TDPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BEN
2
Ligand/Ion
BENZAMIDINE
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
GOL
6
Ligand/Ion
GLYCEROL
4
K
-1
Ligand/Ion
POTASSIUM ION
5
MN
-1
Ligand/Ion
MANGANESE (II) ION
6
TDP
2
Ligand/Ion
THIAMIN DIPHOSPHATE
[
close Hetero Component info
]
Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
GLN A:112 , SER A:161 , PRO A:163 , THR A:166 , GLN A:167 , HOH A:2099
BINDING SITE FOR RESIDUE K A 501
02
AC2
SOFTWARE
GLU A:193 , ASN A:222 , TYR A:224 , TDP A:601 , HOH A:2306
BINDING SITE FOR RESIDUE MN A 503
03
AC3
SOFTWARE
TYR A:113 , TDP A:601 , TYR B:102 , HIS B:146
BINDING SITE FOR RESIDUE CL A 504
04
AC4
SOFTWARE
HIS A:392 , TRP B:330
BINDING SITE FOR RESIDUE CL A 505
05
AC5
SOFTWARE
ARG A:79
BINDING SITE FOR RESIDUE CL A 506
06
AC6
SOFTWARE
BEN A:701
BINDING SITE FOR RESIDUE CL A 507
07
AC7
SOFTWARE
GLY B:128 , LEU B:130 , THR B:131 , CYS B:178 , ASP B:181 , ASN B:183 , HOH B:2145
BINDING SITE FOR RESIDUE K B 502
08
AC8
SOFTWARE
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:503 , CL A:504 , HOH A:2166 , HOH A:2306 , HOH A:2307 , HOH A:2308 , HOH A:2309 , HOH A:2310 , GLU B:46 , LEU B:74 , GLU B:76 , GLN B:98 , TYR B:102
BINDING SITE FOR RESIDUE TDP A 601
09
AC9
SOFTWARE
ILE A:73 , GLU A:76 , GLN A:80 , ARG A:82 , CL A:507 , HOH A:2073
BINDING SITE FOR RESIDUE BEN A 701
10
BC1
SOFTWARE
GLN A:374 , TRP B:260 , THR B:284 , GLU B:290 , THR B:294 , ARG B:309 , HOH B:2258
BINDING SITE FOR RESIDUE GOL B 701
11
BC2
SOFTWARE
LYS A:153 , ARG A:185 , VAL B:88 , THR B:89 , PHE B:125 , HOH B:2079 , HOH B:2112 , HOH B:2259
BINDING SITE FOR RESIDUE GOL B 702
12
BC3
SOFTWARE
ARG B:309 , CYS B:311 , TYR B:313 , HOH B:2260 , HOH B:2261
BINDING SITE FOR RESIDUE GOL B 703
[
close Site info
]
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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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, 3)
Info
All SCOP Domains
1a: SCOP_d1v16a_ (A:)
2a: SCOP_d1v16b1 (B:2-204)
3a: SCOP_d1v16b2 (B:205-342)
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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
:
Branched-chain alpha-keto acid dehydrogenase, PP module
(23)
Human (Homo sapiens) [TaxId: 9606]
(19)
1a
d1v16a_
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
d1v16b1
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
d1v16b2
B:205-342
[
close SCOP info
]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1v16B01 (B:214-338)
2a: CATH_1v16B02 (B:17-213)
2b: CATH_1v16A00 (A:6-400)
View:
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Classes
(
)
(
)
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
1v16B01
B:214-338
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Human (Homo sapiens)
(31)
2a
1v16B02
B:17-213
2b
1v16A00
A:6-400
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_E1_dh_1v16A01 (A:61-361)
2a: PFAM_Transket_pyr_1v16B01 (B:19-197)
3a: PFAM_Transketolase_C_1v16B02 (B:211-329)
View:
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Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
THDP-binding
(106)
Family
:
E1_dh
(27)
Homo sapiens (Human)
(14)
1a
E1_dh-1v16A01
A:61-361
Family
:
Transket_pyr
(45)
Homo sapiens (Human)
(16)
2a
Transket_pyr-1v16B01
B:19-197
Clan
:
no clan defined [family: Transketolase_C]
(40)
Family
:
Transketolase_C
(40)
Homo sapiens (Human)
(16)
3a
Transketolase_C-1v16B02
B:211-329
[
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]
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Asymmetric Unit 1
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