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2PNR
Asym. Unit
Info
Asym.Unit (282 KB)
Biol.Unit 1 (139 KB)
Biol.Unit 2 (140 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF THE ASYMMETRIC PDK3-L2 COMPLEX
Authors
:
D. G. Vassylyev, C. N. Steussy, Y. Devedjiev
Date
:
25 Apr 07 (Deposition) - 21 Aug 07 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,E,F,G
Biol. Unit 1: A,B,C (1x)
Biol. Unit 2: E,F,G (1x)
Keywords
:
Pyruvate Dehydrogenase Kinase 3, Lipoyl-Bearing Domain, Asymmetric Protein-Protein Complex, Transferase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
Y. Devedjiev, C. N. Steussy, D. G. Vassylyev
Crystal Structure Of An Asymmetric Complex Of Pyruvate Dehydrogenase Kinase 3 With Lipoyl Domain 2 And Its Biological Implications
J. Mol. Biol. V. 370 407 2007
(for further references see the
PDB file header
)
[
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Hetero Components
(1, 2)
Info
All Hetero Components
1a: DIHYDROLIPOIC ACID (REDa)
1b: DIHYDROLIPOIC ACID (REDb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
RED
2
Ligand/Ion
DIHYDROLIPOIC ACID
[
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]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:397 , GLN B:31 , PHE B:35 , PHE B:48 , LYS C:173 , HOH C:906
BINDING SITE FOR RESIDUE RED C 900
2
AC2
SOFTWARE
ARG E:397 , LEU F:27 , LYS G:173
BINDING SITE FOR RESIDUE RED G 901
[
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]
SAPs(SNPs)/Variants
(4, 16)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_070081 (K114T, chain A/B/E/F, )
2: VAR_070082 (R158H, chain A/B/E/F, )
3: VAR_042297 (E219A, chain A/B/E/F, )
4: VAR_070083 (Y334S, chain A/B/E/F, )
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/B/E/F
K
114
T
2
UniProt
VAR_070082
R
158
H
PDK3_HUMAN
Disease (CMTX6)
---
A/B/E/F
R
158
H
3
UniProt
VAR_042297
E
219
A
PDK3_HUMAN
Unclassified
---
A/B/E/F
E
219
A
4
UniProt
VAR_070083
Y
334
S
PDK3_HUMAN
Polymorphism
---
A/B/E/F
Y
334
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: LIPOYL (-|C:157-186,G:157-186)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LIPOYL
PS00189
2-oxo acid dehydrogenases acyltransferase component lipoyl binding site.
ODP2_HUMAN
116-145
243-272
2
-
C:157-186
G:157-186
[
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]
Exons
(13, 48)
Info
All Exons
Exon 1.5a (C:135-177 | G:135-177)
Exon 1.6 (C:177-213 | G:177-213)
Exon 2.1a (A:13-36 | B:14-36 | E:13-36 | F:14...)
Exon 2.2b (A:36-83 | B:36-83 | E:36-83 | F:36...)
Exon 2.3a (A:83-107 | B:83-107 | E:83-107 | F...)
Exon 2.4 (A:107-169 | B:107-169 (gaps) | E:1...)
Exon 2.5 (A:169-199 | B:169-199 | E:169-199 ...)
Exon 2.6 (A:199-225 | B:199-225 | E:199-225 ...)
Exon 2.7 (A:225-250 | B:225-250 | E:225-250 ...)
Exon 2.8 (A:251-284 | B:251-284 (gaps) | E:2...)
Exon 2.9 (A:285-321 (gaps) | B:285-304 | E:2...)
Exon 2.10 (A:322-359 | B:327-359 | E:322-359 ...)
Exon 2.11b (A:360-400 | B:360-390 (gaps) | E:3...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.4/1.5a
02: Boundary 1.5a/1.6
03: Boundary 1.6/1.7a
04: Boundary -/2.1a
05: Boundary 2.1a/2.2b
06: Boundary 2.2b/2.3a
07: Boundary 2.3a/2.4
08: Boundary 2.4/2.5
09: Boundary 2.5/2.6
10: Boundary 2.6/2.7
11: Boundary 2.7/2.8
12: Boundary 2.8/2.9
13: Boundary 2.9/2.10
14: Boundary 2.10/2.11b
15: 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
0
-
-
1.5a
ENST00000280346
5a
ENSE00001127996
chr11:
111904128-111904254
127
ODP2_HUMAN
221-263
43
2
C:135-177
G:135-177
43
43
1.6
ENST00000280346
6
ENSE00001127990
chr11:
111907997-111908184
188
ODP2_HUMAN
263-325
63
2
C:177-213
G:177-213
37
37
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
4
A:13-36
B:14-36
E:13-36
F:14-36
24
23
24
23
2.2b
ENST00000379162
2b
ENSE00000863221
X:24512859-24513000
142
PDK3_HUMAN
36-83
48
4
A:36-83
B:36-83
E:36-83
F:36-83
48
48
48
48
2.3a
ENST00000379162
3a
ENSE00000667142
X:24516946-24517017
72
PDK3_HUMAN
83-107
25
4
A:83-107
B:83-107
E:83-107
F:83-107
25
25
25
25
2.4
ENST00000379162
4
ENSE00000667143
X:24521444-24521628
185
PDK3_HUMAN
107-169
63
4
A:107-169
B:107-169 (gaps)
E:107-169
F:107-169 (gaps)
63
63
63
63
2.5
ENST00000379162
5
ENSE00000667144
X:24523326-24523415
90
PDK3_HUMAN
169-199
31
4
A:169-199
B:169-199
E:169-199
F:169-199
31
31
31
31
2.6
ENST00000379162
6
ENSE00001259254
X:24537050-24537127
78
PDK3_HUMAN
199-225
27
4
A:199-225
B:199-225
E:199-225
F:199-225
27
27
27
27
2.7
ENST00000379162
7
ENSE00000667146
X:24544315-24544391
77
PDK3_HUMAN
225-250
26
4
A:225-250
B:225-250
E:225-250
F:225-250
26
26
26
26
2.8
ENST00000379162
8
ENSE00000370908
X:24545691-24545792
102
PDK3_HUMAN
251-284
34
4
A:251-284
B:251-284 (gaps)
E:251-284
F:251-284 (gaps)
34
34
34
34
2.9
ENST00000379162
9
ENSE00000667176
X:24546193-24546303
111
PDK3_HUMAN
285-321
37
4
A:285-321 (gaps)
B:285-304
E:285-321 (gaps)
F:285-304
37
20
37
20
2.10
ENST00000379162
10
ENSE00000370910
X:24549774-24549887
114
PDK3_HUMAN
322-359
38
4
A:322-359
B:327-359
E:322-359
F:327-359
38
33
38
33
2.11b
ENST00000379162
11b
ENSE00001857428
X:24552046-24552542
497
PDK3_HUMAN
360-406
47
4
A:360-400
B:360-390 (gaps)
E:360-400
F:360-390 (gaps)
41
31
41
31
[
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]
SCOP Domains
(3, 10)
Info
All SCOP Domains
1a: SCOP_d2pnra1 (A:13-176)
1b: SCOP_d2pnrb1 (B:14-173)
1c: SCOP_d2pnre1 (E:13-176)
1d: SCOP_d2pnrf1 (F:14-173)
2a: SCOP_d2pnrc_ (C:)
2b: SCOP_d2pnrg_ (G:)
3a: SCOP_d2pnra2 (A:177-301)
3b: SCOP_d2pnrb2 (B:174-390)
3c: SCOP_d2pnre2 (E:177-301)
3d: SCOP_d2pnrf2 (F:174-390)
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)
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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
d2pnra1
A:13-176
1b
d2pnrb1
B:14-173
1c
d2pnre1
E:13-176
1d
d2pnrf1
F:14-173
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
d2pnrc_
C:
2b
d2pnrg_
G:
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
d2pnra2
A:177-301
3b
d2pnrb2
B:174-390
3c
d2pnre2
E:177-301
3d
d2pnrf2
F:174-390
[
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]
CATH Domains
(2, 8)
Info
all CATH domains
1a: CATH_2pnrA02 (A:184-368)
1b: CATH_2pnrE02 (E:184-368)
1c: CATH_2pnrB02 (B:184-368)
1d: CATH_2pnrF02 (F:184-368)
2a: CATH_2pnrA01 (A:13-172)
2b: CATH_2pnrE01 (E:13-172)
2c: CATH_2pnrB01 (B:14-172)
2d: CATH_2pnrF01 (F:14-172)
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Organisms
(
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(
)
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
2pnrA02
A:184-368
1b
2pnrE02
E:184-368
1c
2pnrB02
B:184-368
1d
2pnrF02
F: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
2pnrA01
A:13-172
2b
2pnrE01
E:13-172
2c
2pnrB01
B:14-172
2d
2pnrF01
F:14-172
[
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Pfam Domains
(3, 10)
Info
all PFAM domains
1a: PFAM_HATPase_c_2pnrF01 (F:236-361)
1b: PFAM_HATPase_c_2pnrF02 (F:236-361)
1c: PFAM_HATPase_c_2pnrF03 (F:236-361)
1d: PFAM_HATPase_c_2pnrF04 (F:236-361)
2a: PFAM_Biotin_lipoyl_2pnrG01 (G:135-207)
2b: PFAM_Biotin_lipoyl_2pnrG02 (G:135-207)
3a: PFAM_BCDHK_Adom3_2pnrF05 (F:25-189)
3b: PFAM_BCDHK_Adom3_2pnrF06 (F:25-189)
3c: PFAM_BCDHK_Adom3_2pnrF07 (F:25-189)
3d: PFAM_BCDHK_Adom3_2pnrF08 (F:25-189)
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Clans
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Organisms
(
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(
)
Clan
:
His_Kinase_A
(147)
Family
:
HATPase_c
(132)
Homo sapiens (Human)
(95)
1a
HATPase_c-2pnrF01
F:236-361
1b
HATPase_c-2pnrF02
F:236-361
1c
HATPase_c-2pnrF03
F:236-361
1d
HATPase_c-2pnrF04
F:236-361
Clan
:
Hybrid
(58)
Family
:
Biotin_lipoyl
(16)
Homo sapiens (Human)
(8)
2a
Biotin_lipoyl-2pnrG01
G:135-207
2b
Biotin_lipoyl-2pnrG02
G:135-207
Clan
:
no clan defined [family: BCDHK_Adom3]
(12)
Family
:
BCDHK_Adom3
(12)
Homo sapiens (Human)
(11)
3a
BCDHK_Adom3-2pnrF05
F:25-189
3b
BCDHK_Adom3-2pnrF06
F:25-189
3c
BCDHK_Adom3-2pnrF07
F:25-189
3d
BCDHK_Adom3-2pnrF08
F:25-189
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