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2VQM
Asym. Unit
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Asym.Unit (75 KB)
Biol.Unit 1 (69 KB)
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(1)
Title
:
STRUCTURE OF HDAC4 CATALYTIC DOMAIN BOUND TO A HYDROXAMIC ACID INHBITOR
Authors
:
M. J. Bottomley, P. Lo Surdo, P. Di Giovine, A. Cirillo, R. Scarpelli, F. Ferrigno, P. Jones, P. Neddermann, R. De Francesco, C. Steinkuhler, P. Gallinari, A. Carfi
Date
:
17 Mar 08 (Deposition) - 08 Jul 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Inhibitor, Repressor, Chromatin, Coiled Coil, Histone Deacetylase, Transcription Regulation, Ubl Conjugation, Chromatin Regulator, Polymorphism, Transcription, Phosphoprotein, Hdac, Zinc, Hdaci, Nucleus, Hydrolase, Cytoplasm
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. J. Bottomley, P. Lo Surdo, P. Di Giovine, A. Cirillo, R. Scarpelli, F. Ferrigno, P. Jones, P. Neddermann, R. De Francesco, C. Steinkuhler, P. Gallinari, A. Carfi
Structural And Functional Analysis Of The Human Hdac4 Catalytic Domain Reveals A Regulatory Zinc-Binding Domain.
J. Biol. Chem. V. 283 26694 2008
[
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Hetero Components
(3, 5)
Info
All Hetero Components
1a: N-HYDROXY-5-[(3-PHENYL-5,6-DIHYDRO... (HA3a)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
HA3
1
Ligand/Ion
N-HYDROXY-5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHENE-2-CARBOXAMIDE
2
K
2
Ligand/Ion
POTASSIUM ION
3
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
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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
ASP A:194 , ASP A:196 , HIS A:198 , SER A:217 , LEU A:218
BINDING SITE FOR RESIDUE K A1408
2
AC2
SOFTWARE
PHE A:207 , ASP A:210 , VAL A:213 , PHE A:244 , HOH A:2235 , HOH A:2236
BINDING SITE FOR RESIDUE K A1409
3
AC3
SOFTWARE
LEU A:78 , TYR A:79 , VAL A:121 , ALA A:124 , PRO A:156 , GLY A:167 , PHE A:168 , HIS A:198 , PHE A:227 , ASP A:290 , GLY A:330 , ZN A:1411 , HOH A:2296 , HOH A:2372 , HOH A:2373 , HOH A:2375
BINDING SITE FOR RESIDUE HA3 A1410
4
AC4
SOFTWARE
ASP A:196 , HIS A:198 , ASP A:290 , HA3 A:1410 , HOH A:2375
BINDING SITE FOR RESIDUE ZN A1411
5
AC5
SOFTWARE
HIS A:21 , CYS A:23 , HIS A:34 , CYS A:107
BINDING SITE FOR RESIDUE ZN A1412
[
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SAPs(SNPs)/Variants
(2, 2)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_036042 (P83R, chain A, )
2: VAR_071965 (V110I, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_036042
P
727
R
HDAC4_HUMAN
Unclassified
---
A
P
83
R
2
UniProt
VAR_071965
V
754
I
HDAC4_HUMAN
Polymorphism
---
A
V
110
I
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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Label:
End label:
Sorry, no Info available
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Exons
(13, 13)
Info
All Exons
Exon 1.22 (A:6-11)
Exon 1.23a (A:11-55 (gaps))
Exon 1.24a (A:56-96 (gaps))
Exon 1.25a (A:96-111)
Exon 1.27a (A:112-147)
Exon 1.28 (A:148-166)
Exon 1.29 (A:166-195)
Exon 1.30 (A:196-235)
Exon 1.31a (A:236-268)
Exon 1.32 (A:268-308)
Exon 1.33b (A:308-352)
Exon 1.35 (A:353-381)
Exon 1.36 (A:381-407)
View:
Select:
Label:
All Exon Boundaries
01: Boundary 1.21/1.22
02: Boundary 1.22/1.23a
03: Boundary 1.23a/1.24a
04: Boundary 1.24a/1.25a
05: Boundary 1.25a/1.27a
06: Boundary 1.27a/1.28
07: Boundary 1.28/1.29
08: Boundary 1.29/1.30
09: Boundary 1.30/1.31a
10: Boundary 1.31a/1.32
11: Boundary 1.32/1.33b
12: Boundary 1.33b/1.35
13: Boundary 1.35/1.36
14: Boundary 1.36/1.37c
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
1.3
ENST00000345617
3
ENSE00001242645
chr2:
240322643-240322071
573
HDAC4_HUMAN
-
0
0
-
-
1.4
ENST00000345617
4
ENSE00002161358
chr2:
240274613-240274373
241
HDAC4_HUMAN
1-8
8
0
-
-
1.7b
ENST00000345617
7b
ENSE00001679522
chr2:
240158360-240158289
72
HDAC4_HUMAN
8-32
25
0
-
-
1.9a
ENST00000345617
9a
ENSE00001308711
chr2:
240111773-240111529
245
HDAC4_HUMAN
32-113
82
0
-
-
1.11b
ENST00000345617
11b
ENSE00001753193
chr2:
240098259-240098109
151
HDAC4_HUMAN
114-164
51
0
-
-
1.12b
ENST00000345617
12b
ENSE00001708242
chr2:
240085619-240085499
121
HDAC4_HUMAN
164-204
41
0
-
-
1.13
ENST00000345617
13
ENSE00001658039
chr2:
240078469-240078348
122
HDAC4_HUMAN
204-245
42
0
-
-
1.15
ENST00000345617
15
ENSE00001780577
chr2:
240066410-240066279
132
HDAC4_HUMAN
245-289
45
0
-
-
1.17
ENST00000345617
17
ENSE00001723920
chr2:
240061492-240061380
113
HDAC4_HUMAN
289-326
38
0
-
-
1.18
ENST00000345617
18
ENSE00001752779
chr2:
240056339-240056223
117
HDAC4_HUMAN
327-365
39
0
-
-
1.19b
ENST00000345617
19b
ENSE00001593963
chr2:
240056139-240055941
199
HDAC4_HUMAN
366-432
67
0
-
-
1.20c
ENST00000345617
20c
ENSE00000787258
chr2:
240048375-240048152
224
HDAC4_HUMAN
432-506
75
0
-
-
1.21
ENST00000345617
21
ENSE00001607824
chr2:
240037006-240036749
258
HDAC4_HUMAN
507-592
86
0
-
-
1.22
ENST00000345617
22
ENSE00001621125
chr2:
240033408-240033222
187
HDAC4_HUMAN
593-655
63
1
A:6-11
6
1.23a
ENST00000345617
23a
ENSE00001779179
chr2:
240029879-240029746
134
HDAC4_HUMAN
655-699
45
1
A:11-55 (gaps)
45
1.24a
ENST00000345617
24a
ENSE00001735120
chr2:
240024592-240024472
121
HDAC4_HUMAN
700-740
41
1
A:56-96 (gaps)
41
1.25a
ENST00000345617
25a
ENSE00001623395
chr2:
240016752-240016706
47
HDAC4_HUMAN
740-755
16
1
A:96-111
16
1.27a
ENST00000345617
27a
ENSE00001710463
chr2:
240011812-240011705
108
HDAC4_HUMAN
756-791
36
1
A:112-147
36
1.28
ENST00000345617
28
ENSE00001659227
chr2:
240009310-240009255
56
HDAC4_HUMAN
792-810
19
1
A:148-166
19
1.29
ENST00000345617
29
ENSE00001595029
chr2:
240005938-240005851
88
HDAC4_HUMAN
810-839
30
1
A:166-195
30
1.30
ENST00000345617
30
ENSE00001598022
chr2:
240003917-240003798
120
HDAC4_HUMAN
840-879
40
1
A:196-235
40
1.31a
ENST00000345617
31a
ENSE00001725968
chr2:
240002888-240002791
98
HDAC4_HUMAN
880-912
33
1
A:236-268
33
1.32
ENST00000345617
32
ENSE00001643358
chr2:
239990303-239990185
119
HDAC4_HUMAN
912-952
41
1
A:268-308
41
1.33b
ENST00000345617
33b
ENSE00001679613
chr2:
239988551-239988418
134
HDAC4_HUMAN
952-996
45
1
A:308-352
45
1.35
ENST00000345617
35
ENSE00001784017
chr2:
239976529-239976445
85
HDAC4_HUMAN
997-1025
29
1
A:353-381
29
1.36
ENST00000345617
36
ENSE00001770463
chr2:
239975297-239975156
142
HDAC4_HUMAN
1025-1072
48
1
A:381-407
27
1.37c
ENST00000345617
37c
ENSE00001207161
chr2:
239974832-239969864
4969
HDAC4_HUMAN
1072-1084
13
0
-
-
[
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SCOP Domains
(0, 0)
Info
All SCOP Domains
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Sorry, no Info available
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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Asymmetric Unit 1
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