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3D2R
Asym. Unit
Info
Asym.Unit (130 KB)
Biol.Unit 1 (123 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF PYRUVATE DEHYDROGENASE KINASE ISOFORM 4 IN COMPLEX WITH ADP
Authors
:
M. Kato, R. M. Wynn, L. C. Chuang, S. -C. Tso, J. Li, D. T. Chuang
Date
:
08 May 08 (Deposition) - 05 Aug 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.03
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Protein-Nucleotide Complex, Homodimer, Ghkl Superfamily, Kinase, Carbohydrate Metabolism, Glucose Metabolism, Mitochondrion, Phosphoprotein, Transferase, Transit Peptide
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. M. Wynn, M. Kato, J. L. Chuang, S. C. Tso, J. Li, D. T. Chuang
Pyruvate Dehydrogenase Kinase-4 Structures Reveal A Metastable Open Conformation Fostering Robust Core-Free Basal Activity.
J. Biol. Chem. V. 283 25305 2008
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
GOL
2
Ligand/Ion
GLYCEROL
3
MG
2
Ligand/Ion
MAGNESIUM ION
[
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:258
BINDING SITE FOR RESIDUE MG A 500
2
AC2
SOFTWARE
ASN B:258
BINDING SITE FOR RESIDUE MG B 500
3
AC3
SOFTWARE
ASN A:258 , ARG A:261 , ALA A:262 , ASP A:293 , LEU A:306 , TYR A:311 , SER A:312 , THR A:313 , ALA A:328 , GLY A:329 , PHE A:330 , GLY A:331 , GLY A:333 , LEU A:334 , THR A:358
BINDING SITE FOR RESIDUE ADP A 501
4
AC4
SOFTWARE
ASN B:258 , ARG B:261 , ALA B:262 , ASP B:293 , LEU B:306 , TYR B:311 , SER B:312 , THR B:313 , ALA B:328 , GLY B:329 , PHE B:330 , GLY B:331 , GLY B:333 , LEU B:334 , THR B:358
BINDING SITE FOR RESIDUE ADP B 501
5
AC5
SOFTWARE
ASP A:160 , LYS A:342 , LYS A:374 , TRP B:395
BINDING SITE FOR RESIDUE GOL A 502
6
AC6
SOFTWARE
TRP A:395 , ASP B:160 , LEU B:339 , LYS B:342 , LYS B:374
BINDING SITE FOR RESIDUE GOL B 502
[
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SAPs(SNPs)/Variants
(1, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_042300 (D109G, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_042300
D
109
G
PDK4_HUMAN
Polymorphism
34898343
A/B
D
109
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
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End label:
Sorry, no Info available
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Exons
(11, 22)
Info
All Exons
Exon 1.1a (A:21-44 | B:20-44)
Exon 1.2a (A:44-91 (gaps) | B:44-91)
Exon 1.3 (A:91-115 | B:91-115)
Exon 1.4a (A:115-177 (gaps) | B:115-177 (gaps...)
Exon 1.4c (A:177-206 (gaps) | B:177-206)
Exon 1.5 (A:206-232 | B:206-232)
Exon 1.6b (A:232-257 | B:232-257)
Exon 1.7a (A:258-290 | B:258-290)
Exon 1.7d (A:291-327 (gaps) | B:291-327 (gaps...)
Exon 1.8a (A:328-365 | B:328-365)
Exon 1.9b (A:366-397 (gaps) | B:366-397 (gaps...)
View:
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All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.2a
03: Boundary 1.2a/1.3
04: Boundary 1.3/1.4a
05: Boundary 1.4a/1.4c
06: Boundary 1.4c/1.5
07: Boundary 1.5/1.6b
08: Boundary 1.6b/1.7a
09: Boundary 1.7a/1.7d
10: Boundary 1.7d/1.8a
11: Boundary 1.8a/1.9b
12: Boundary 1.9b/-
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
ENST00000005178
1a
ENSE00001133344
chr7:
95225803-95225476
328
PDK4_HUMAN
1-44
44
2
A:21-44
B:20-44
24
25
1.2a
ENST00000005178
2a
ENSE00000706270
chr7:
95224476-95224335
142
PDK4_HUMAN
44-91
48
2
A:44-91 (gaps)
B:44-91
48
48
1.3
ENST00000005178
3
ENSE00000706269
chr7:
95223082-95223011
72
PDK4_HUMAN
91-115
25
2
A:91-115
B:91-115
25
25
1.4a
ENST00000005178
4a
ENSE00000706268
chr7:
95222256-95222072
185
PDK4_HUMAN
115-177
63
2
A:115-177 (gaps)
B:115-177 (gaps)
63
63
1.4c
ENST00000005178
4c
ENSE00000706266
chr7:
95221909-95221823
87
PDK4_HUMAN
177-206
30
2
A:177-206 (gaps)
B:177-206
30
30
1.5
ENST00000005178
5
ENSE00000706265
chr7:
95221377-95221300
78
PDK4_HUMAN
206-232
27
2
A:206-232
B:206-232
27
27
1.6b
ENST00000005178
6b
ENSE00000706264
chr7:
95219028-95218952
77
PDK4_HUMAN
232-257
26
2
A:232-257
B:232-257
26
26
1.7a
ENST00000005178
7a
ENSE00000706262
chr7:
95217137-95217039
99
PDK4_HUMAN
258-290
33
2
A:258-290
B:258-290
33
33
1.7d
ENST00000005178
7d
ENSE00000706260
chr7:
95216840-95216730
111
PDK4_HUMAN
291-327
37
2
A:291-327 (gaps)
B:291-327 (gaps)
37
37
1.8a
ENST00000005178
8a
ENSE00000706258
chr7:
95216435-95216322
114
PDK4_HUMAN
328-365
38
2
A:328-365
B:328-365
38
38
1.9b
ENST00000005178
9b
ENSE00001267271
chr7:
95215093-95212811
2283
PDK4_HUMAN
366-411
46
2
A:366-397 (gaps)
B:366-397 (gaps)
32
32
[
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SCOP Domains
(2, 4)
Info
All SCOP Domains
1a: SCOP_d3d2ra1 (A:21-180)
1b: SCOP_d3d2rb1 (B:20-180)
2a: SCOP_d3d2ra2 (A:181-397)
2b: SCOP_d3d2rb2 (B:181-397)
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Protein Domains
(
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(
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Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Bromodomain-like
(339)
Superfamily
:
alpha-ketoacid dehydrogenase kinase, N-terminal domain
(40)
Family
:
automated matches
(20)
Protein domain
:
automated matches
(20)
Human (Homo sapiens) [TaxId: 9606]
(8)
1a
d3d2ra1
A:21-180
1b
d3d2rb1
B:20-180
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
:
automated matches
(42)
Protein domain
:
automated matches
(42)
Human (Homo sapiens) [TaxId: 9606]
(10)
2a
d3d2ra2
A:181-397
2b
d3d2rb2
B:181-397
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CATH Domains
(2, 4)
Info
all CATH domains
1a: CATH_3d2rA02 (A:190-374)
1b: CATH_3d2rB02 (B:190-374)
2a: CATH_3d2rA01 (A:21-189)
2b: CATH_3d2rB01 (B:20-189)
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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)
Homo sapiens. Organism_taxid: 9606.
(3)
1a
3d2rA02
A:190-374
1b
3d2rB02
B:190-374
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)
Homo sapiens. Organism_taxid: 9606.
(1)
2a
3d2rA01
A:21-189
2b
3d2rB01
B:20-189
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Asymmetric Unit 1
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