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1Y8O
Asym. Unit
Info
Asym.Unit (87 KB)
Biol.Unit 1 (158 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE PDK3-L2 COMPLEX
Authors
:
M. Kato, J. L. Chuang, R. M. Wynn, D. T. Chuang
Date
:
13 Dec 04 (Deposition) - 24 May 05 (Release) - 05 Oct 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.48
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Pyruvate Dehydrogenase Kinase 3, Lipoyl-Bearing Domain, Protein- Protein Complex, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Kato, J. L. Chuang, S. C. Tso, R. M. Wynn, D. T. Chuang
Crystal Structure Of Pyruvate Dehydrogenase Kinase 3 Bound To Lipoyl Domain 2 Of Human Pyruvate Dehydrogenase Complex.
Embo J. V. 24 1763 2005
[
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]
Hetero Components
(4, 5)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
3a: MAGNESIUM ION (MGa)
4a: DIHYDROLIPOIC ACID (REDa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
K
2
Ligand/Ion
POTASSIUM ION
3
MG
1
Ligand/Ion
MAGNESIUM ION
4
RED
1
Ligand/Ion
DIHYDROLIPOIC ACID
[
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]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:247 , LYS A:250 , ASN A:251 , ADP A:504 , HOH A:544 , HOH A:560
BINDING SITE FOR RESIDUE MG A 501
2
AC2
SOFTWARE
LEU A:300 , ASN A:302 , SER A:306 , GLY A:325 , ADP A:504
BINDING SITE FOR RESIDUE K A 502
3
AC3
SOFTWARE
SER A:20 , ARG A:21 , PHE A:22 , ASN A:59 , PHE A:372
BINDING SITE FOR RESIDUE K A 503
4
AC4
SOFTWARE
SER A:45 , PHE A:48 , LYS B:173
BINDING SITE FOR RESIDUE RED B 373
5
AC5
SOFTWARE
ASN A:251 , ARG A:254 , ALA A:255 , ASP A:287 , VAL A:292 , LEU A:300 , PHE A:324 , GLY A:325 , LEU A:328 , THR A:352 , MG A:501 , K A:502 , HOH A:514 , HOH A:531 , HOH A:544 , HOH A:560
BINDING SITE FOR RESIDUE ADP A 504
[
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]
SAPs(SNPs)/Variants
(5, 5)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_070081 (K114T, chain A, )
2: VAR_070082 (R158H, chain A, )
3: VAR_042297 (E219A, chain A, )
4: VAR_047414 (D227V, chain B, )
5: 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_047414
D
313
V
ODP2_HUMAN
Polymorphism
11553592
B
D
227
V
5
UniProt
VAR_070083
Y
334
S
PDK3_HUMAN
Polymorphism
---
A
Y
334
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: BIOTINYL_LIPOYL (-|B:132-208)
2: LIPOYL (-|B:157-186)
;
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
1
-
B:132-208
2
LIPOYL
PS00189
2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.
ODP2_HUMAN
116-145
243-272
1
-
B:157-186
[
close PROSITE info
]
Exons
(14, 14)
Info
All Exons
Exon 1.4 (B:128-134)
Exon 1.5a (B:135-177)
Exon 1.6 (B:177-229 (gaps))
Exon 2.1a (A:13-36)
Exon 2.2b (A:36-83)
Exon 2.3a (A:83-107)
Exon 2.4 (A:107-169)
Exon 2.5 (A:169-199)
Exon 2.6 (A:199-225)
Exon 2.7 (A:225-250)
Exon 2.8 (A:251-284)
Exon 2.9 (A:285-321 (gaps))
Exon 2.10 (A:324-359)
Exon 2.11b (A:360-401)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.3b/1.4
02: Boundary 1.4/1.5a
03: Boundary 1.5a/1.6
04: Boundary 1.6/1.7a
05: Boundary -/2.1a
06: Boundary 2.1a/2.2b
07: Boundary 2.2b/2.3a
08: Boundary 2.3a/2.4
09: Boundary 2.4/2.5
10: Boundary 2.5/2.6
11: Boundary 2.6/2.7
12: Boundary 2.7/2.8
13: Boundary 2.8/2.9
14: Boundary 2.9/2.10
15: Boundary 2.10/2.11b
16: Boundary 2.11b/-
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
ENST00000280346
1a
ENSE00001130691
chr11:
111895538-111896475
938
ODP2_HUMAN
1-93
93
0
-
-
1.2b
ENST00000280346
2b
ENSE00000996256
chr11:
111896922-111897023
102
ODP2_HUMAN
94-127
34
0
-
-
1.3b
ENST00000280346
3b
ENSE00001105302
chr11:
111899239-111899363
125
ODP2_HUMAN
128-169
42
0
-
-
1.4
ENST00000280346
4
ENSE00001128003
chr11:
111899516-111899669
154
ODP2_HUMAN
169-220
52
1
B:128-134
7
1.5a
ENST00000280346
5a
ENSE00001127996
chr11:
111904128-111904254
127
ODP2_HUMAN
221-263
43
1
B:135-177
43
1.6
ENST00000280346
6
ENSE00001127990
chr11:
111907997-111908184
188
ODP2_HUMAN
263-325
63
1
B:177-229 (gaps)
53
1.7a
ENST00000280346
7a
ENSE00001127984
chr11:
111909968-111910121
154
ODP2_HUMAN
326-377
52
0
-
-
1.8
ENST00000280346
8
ENSE00001127976
chr11:
111914190-111914257
68
ODP2_HUMAN
377-399
23
0
-
-
1.9
ENST00000280346
9
ENSE00001127968
chr11:
111915862-111915954
93
ODP2_HUMAN
400-430
31
0
-
-
1.10
ENST00000280346
10
ENSE00001127959
chr11:
111916587-111916694
108
ODP2_HUMAN
431-466
36
0
-
-
1.11
ENST00000280346
11
ENSE00000996257
chr11:
111921958-111922073
116
ODP2_HUMAN
467-505
39
0
-
-
1.12a
ENST00000280346
12a
ENSE00000996239
chr11:
111930627-111930789
163
ODP2_HUMAN
505-559
55
0
-
-
1.13a
ENST00000280346
13a
ENSE00000996255
chr11:
111931762-111931898
137
ODP2_HUMAN
560-605
46
0
-
-
1.14d
ENST00000280346
14d
ENSE00001514061
chr11:
111933130-111935114
1985
ODP2_HUMAN
605-647
43
0
-
-
2.1a
ENST00000379162
1a
ENSE00001844757
X:24483338-24483678
341
PDK3_HUMAN
1-36
36
1
A:13-36
24
2.2b
ENST00000379162
2b
ENSE00000863221
X:24512859-24513000
142
PDK3_HUMAN
36-83
48
1
A:36-83
48
2.3a
ENST00000379162
3a
ENSE00000667142
X:24516946-24517017
72
PDK3_HUMAN
83-107
25
1
A:83-107
25
2.4
ENST00000379162
4
ENSE00000667143
X:24521444-24521628
185
PDK3_HUMAN
107-169
63
1
A:107-169
63
2.5
ENST00000379162
5
ENSE00000667144
X:24523326-24523415
90
PDK3_HUMAN
169-199
31
1
A:169-199
31
2.6
ENST00000379162
6
ENSE00001259254
X:24537050-24537127
78
PDK3_HUMAN
199-225
27
1
A:199-225
27
2.7
ENST00000379162
7
ENSE00000667146
X:24544315-24544391
77
PDK3_HUMAN
225-250
26
1
A:225-250
26
2.8
ENST00000379162
8
ENSE00000370908
X:24545691-24545792
102
PDK3_HUMAN
251-284
34
1
A:251-284
34
2.9
ENST00000379162
9
ENSE00000667176
X:24546193-24546303
111
PDK3_HUMAN
285-321
37
1
A:285-321 (gaps)
37
2.10
ENST00000379162
10
ENSE00000370910
X:24549774-24549887
114
PDK3_HUMAN
322-359
38
1
A:324-359
36
2.11b
ENST00000379162
11b
ENSE00001857428
X:24552046-24552542
497
PDK3_HUMAN
360-406
47
1
A:360-401
42
[
close EXON info
]
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1y8oa1 (A:13-176)
2a: SCOP_d1y8ob_ (B:)
3a: SCOP_d1y8oa2 (A:177-301)
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)
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Folds
(
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(
)
Superfamilies
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(
)
Families
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)
(
)
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
d1y8oa1
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
d1y8ob_
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
d1y8oa2
A:177-301
[
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]
CATH Domains
(2, 2)
Info
all CATH domains
1a: CATH_1y8oA02 (A:184-368)
2a: CATH_1y8oA01 (A:13-172)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
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
1y8oA02
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
1y8oA01
A:13-172
[
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Pfam Domains
(3, 3)
Info
all PFAM domains
1a: PFAM_HATPase_c_1y8oA01 (A:236-361)
2a: PFAM_Biotin_lipoyl_1y8oB01 (B:133-207)
3a: PFAM_BCDHK_Adom3_1y8oA02 (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-1y8oA01
A:236-361
Clan
:
Hybrid
(58)
Family
:
Biotin_lipoyl
(16)
Homo sapiens (Human)
(8)
2a
Biotin_lipoyl-1y8oB01
B:133-207
Clan
:
no clan defined [family: BCDHK_Adom3]
(12)
Family
:
BCDHK_Adom3
(12)
Homo sapiens (Human)
(11)
3a
BCDHK_Adom3-1y8oA02
A:25-189
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