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2Q8I
Biol. Unit 1
Info
Asym.Unit (86 KB)
Biol.Unit 1 (156 KB)
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(1)
Title
:
PYRUVATE DEHYDROGENASE KINASE ISOFORM 3 IN COMPLEX WITH ANTITUMOR DRUG RADICICOL
Authors
:
M. Kato, J. Li, J. L. Chuang, D. T. Chuang
Date
:
10 Jun 07 (Deposition) - 24 Jul 07 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.60
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Ghkl Atpase/Kinase Family, Pyruvate Dehydrogenase Complex, Mitochondrial Kinase, Radicicol, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Kato, J. Li, J. L. Chuang, D. T. Chuang
Distinct Structural Mechanisms For Inhibition Of Pyruvate Dehydrogenase Kinase Isoforms By Azd7545, Dichloroacetate, And Radicicol.
Structure V. 15 992 2007
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
2a: POTASSIUM ION (Ka)
3a: RADICICOL (RDCa)
4a: DIHYDROLIPOIC ACID (REDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
2
Ligand/Ion
GLYCEROL
2
K
-1
Ligand/Ion
POTASSIUM ION
3
RDC
2
Ligand/Ion
RADICICOL
4
RED
2
Ligand/Ion
DIHYDROLIPOIC ACID
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
SER A:20 , ARG A:21 , PHE A:22 , ASN A:59 , PHE A:372
BINDING SITE FOR RESIDUE K A 407
2
AC2
SOFTWARE
PHE A:48 , ARG A:397 , LYS B:173
BINDING SITE FOR RESIDUE RED B 300
3
AC3
SOFTWARE
LEU A:248 , ASN A:251 , SER A:252 , ALA A:255 , ASP A:287 , VAL A:292 , LEU A:300 , LEU A:328 , THR A:352 , HOH A:431 , HOH A:453 , HOH A:475
BINDING SITE FOR RESIDUE RDC A 408
4
AC4
SOFTWARE
PHE A:301 , LYS A:343 , LEU A:344 , TYR A:345 , HOH A:419
BINDING SITE FOR RESIDUE GOL A 409
[
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SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_070081 (K114T, chain A, )
2: VAR_070082 (R158H, chain A, )
3: VAR_042297 (E219A, chain A, )
4: VAR_070083 (Y334S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_070081
K
114
T
PDK3_HUMAN
Polymorphism
146331370
A
K
114
T
2
UniProt
VAR_070082
R
158
H
PDK3_HUMAN
Disease (CMTX6)
---
A
R
158
H
3
UniProt
VAR_042297
E
219
A
PDK3_HUMAN
Unclassified
---
A
E
219
A
4
UniProt
VAR_070083
Y
334
S
PDK3_HUMAN
Polymorphism
---
A
Y
334
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(2, 4)
Info
All PROSITE Patterns/Profiles
1: BIOTINYL_LIPOYL ()
2: LIPOYL ()
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
BIOTINYL_LIPOYL
PS50968
Biotinyl/lipoyl domain profile.
ODP2_HUMAN
91-167
218-294
2
-
B:132-208
2
LIPOYL
PS00189
2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.
ODP2_HUMAN
116-145
243-272
2
-
B:157-186
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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_d2q8ia1 (A:13-176)
2a: SCOP_d2q8ib_ (B:)
3a: SCOP_d2q8ia2 (A:177-301)
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(
)
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(
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Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
alpha-ketoacid dehydrogenase kinase, N-terminal domain
(40)
Family
:
alpha-ketoacid dehydrogenase kinase, N-terminal domain
(20)
Protein domain
:
Pyruvate dehydrogenase kinase
(6)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d2q8ia1
A:13-176
Class
:
All beta proteins
(24004)
Fold
:
Barrel-sandwich hybrid
(185)
Superfamily
:
Single hybrid motif
(49)
Family
:
Biotinyl/lipoyl-carrier proteins and domains
(40)
Protein domain
:
Lipoyl domain of dihydrolipoamide acetyltransferase
(14)
Human (Homo sapiens) [TaxId: 9606]
(8)
2a
d2q8ib_
B:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
(364)
Superfamily
:
ATPase domain of HSP90 chaperone/DNA topoisomerase II/histidine kinase
(364)
Family
:
alpha-ketoacid dehydrogenase kinase, C-terminal domain
(31)
Protein domain
:
Pyruvate dehydrogenase kinase
(6)
Human (Homo sapiens) [TaxId: 9606]
(5)
3a
d2q8ia2
A:177-301
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CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_2q8iA02 (A:184-368)
2a: CATH_2q8iA01 (A:13-172)
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)
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(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Heat Shock Protein 90
(209)
Homologous Superfamily
:
[code=3.30.565.10, no name defined]
(205)
Human (Homo sapiens)
(95)
1a
2q8iA02
A:184-368
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Butyryl-CoA Dehydrogenase, subunit A; domain 3
(76)
Homologous Superfamily
:
[code=1.20.140.20, no name defined]
(25)
Human (Homo sapiens)
(18)
2a
2q8iA01
A:13-172
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Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_HATPase_c_2q8iA01 (A:236-361)
2a: PFAM_Biotin_lipoyl_2q8iB01 (B:133-207)
3a: PFAM_BCDHK_Adom3_2q8iA02 (A:25-189)
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Clans
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Families
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(
)
Organisms
(
)
(
)
Clan
:
His_Kinase_A
(147)
Family
:
HATPase_c
(132)
Homo sapiens (Human)
(95)
1a
HATPase_c-2q8iA01
A:236-361
Clan
:
Hybrid
(58)
Family
:
Biotin_lipoyl
(16)
Homo sapiens (Human)
(8)
2a
Biotin_lipoyl-2q8iB01
B:133-207
Clan
:
no clan defined [family: BCDHK_Adom3]
(12)
Family
:
BCDHK_Adom3
(12)
Homo sapiens (Human)
(11)
3a
BCDHK_Adom3-2q8iA02
A:25-189
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select residue range 5 to 10 in chain 'A'
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