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1V1R
Biol. Unit 1
Info
Asym.Unit (134 KB)
Biol.Unit 1 (249 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
:
22 Apr 04 (Deposition) - 03 Jun 04 (Release) - 27 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Oxidoreductase, Ketoacid Dehydrogenase, Multi-Enzyme Complex, Acylation, Oxidative Decarboxylation, Maple Syrup Urine Disease, Thiamin 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
(2, 6)
Info
All Hetero Components
1a: CHLORIDE ION (CLa)
1b: CHLORIDE ION (CLb)
1c: CHLORIDE ION (CLc)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
5a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CL
-1
Ligand/Ion
CHLORIDE ION
2
GOL
4
Ligand/Ion
GLYCEROL
3
K
-1
Ligand/Ion
POTASSIUM ION
4
NA
-1
Ligand/Ion
SODIUM ION
5
SO4
2
Ligand/Ion
SULFATE ION
[
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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
GLN A:112 , SER A:161 , PRO A:163 , THR A:166 , GLN A:167 , HOH A:2082
BINDING SITE FOR RESIDUE K A1401
2
AC2
SOFTWARE
GLU A:193 , ASN A:222 , SO4 A:1405 , HOH A:2156
BINDING SITE FOR RESIDUE NA A1402
3
AC3
SOFTWARE
GLN A:112 , GLY A:192 , ALA A:195 , SO4 A:1405
BINDING SITE FOR RESIDUE NA A1403
4
AC4
SOFTWARE
GLN A:351
BINDING SITE FOR RESIDUE CL A1404
5
AC5
SOFTWARE
ARG A:114 , GLY A:192 , GLU A:193 , GLY A:194 , ALA A:195 , ARG A:220 , ASN A:222 , NA A:1402 , NA A:1403 , HOH A:2156 , HOH A:2277 , HOH A:2278
BINDING SITE FOR RESIDUE SO4 A1405
6
AC6
SOFTWARE
GLY B:128 , LEU B:130 , THR B:131 , CYS B:178 , ASP B:181 , ASN B:183 , HOH B:2146
BINDING SITE FOR RESIDUE K B1343
7
AC7
SOFTWARE
GLN A:374 , TRP B:260 , THR B:284 , GLU B:290 , THR B:294 , ARG B:309 , HOH B:2251 , HOH B:2252
BINDING SITE FOR RESIDUE GOL B1344
8
AC8
SOFTWARE
ARG B:309 , VAL B:310 , CYS B:311 , TYR B:313 , HOH B:2253
BINDING SITE FOR RESIDUE GOL B1345
[
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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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_d1v1ra_ (A:)
2a: SCOP_d1v1rb1 (B:2-204)
3a: SCOP_d1v1rb2 (B:205-342)
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Classes
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)
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)
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(
)
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
d1v1ra_
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
d1v1rb1
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
d1v1rb2
B:205-342
[
close SCOP info
]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1v1rB01 (B:214-338)
2a: CATH_1v1rB02 (B:17-213)
2b: CATH_1v1rA00 (A:14-400)
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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
1v1rB01
B:214-338
Homologous Superfamily
:
[code=3.40.50.970, no name defined]
(144)
Human (Homo sapiens)
(31)
2a
1v1rB02
B:17-213
2b
1v1rA00
A:14-400
[
close CATH info
]
Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_E1_dh_1v1rA01 (A:61-361)
2a: PFAM_Transket_pyr_1v1rB01 (B:19-197)
3a: PFAM_Transketolase_C_1v1rB02 (B:211-329)
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Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
THDP-binding
(106)
Family
:
E1_dh
(27)
Homo sapiens (Human)
(14)
1a
E1_dh-1v1rA01
A:61-361
Family
:
Transket_pyr
(45)
Homo sapiens (Human)
(16)
2a
Transket_pyr-1v1rB01
B:19-197
Clan
:
no clan defined [family: Transketolase_C]
(40)
Family
:
Transketolase_C
(40)
Homo sapiens (Human)
(16)
3a
Transketolase_C-1v1rB02
B:211-329
[
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]
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(currently selected atoms:
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Asymmetric Unit 1
Asymmetric Unit 2
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