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2VQQ
Biol. Unit 1
Info
Asym.Unit (133 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (66 KB)
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(1)
Title
:
STRUCTURE OF HDAC4 CATALYTIC DOMAIN (A DOUBLE CYSTEINE-TO-ALANINE MUTANT) BOUND TO A TRIFLUOROMETHYLKETONE 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
:
18 Mar 08 (Deposition) - 08 Jul 08 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.90
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (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
(2, 3)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
3a: 2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,... (TFGa)
3b: 2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,... (TFGb)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
SO4
2
Ligand/Ion
SULFATE ION
3
TFG
1
Ligand/Ion
2,2,2-TRIFLUORO-1-{5-[(3-PHENYL-5,6-DIHYDROIMIDAZO[1,2-A]PYRAZIN-7(8H)-YL)CARBONYL]THIOPHEN-2-YL}ETHANE-1,1-DIOL
4
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(7, 7)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC9 (SOFTWARE)
7: BC2 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:20 , ARG A:37 , ILE A:38 , ARG A:154 , HOH A:2012 , HOH A:2266 , HOH A:2267 , HOH A:2268 , HOH B:2099
BINDING SITE FOR RESIDUE SO4 A1406
2
AC2
SOFTWARE
TRP A:42 , GLN A:46 , ARG A:51 , HOH A:2269
BINDING SITE FOR RESIDUE SO4 A1407
3
AC3
SOFTWARE
ASP A:194 , ASP A:196 , HIS A:198 , SER A:217 , LEU A:218
BINDING SITE FOR RESIDUE K A1408
4
AC4
SOFTWARE
PHE A:207 , ASP A:210 , VAL A:213 , PHE A:244 , HOH A:2154 , HOH A:2156
BINDING SITE FOR RESIDUE K A1409
5
AC5
SOFTWARE
PRO A:156 , HIS A:158 , HIS A:159 , GLY A:167 , PHE A:168 , ASP A:196 , HIS A:198 , PHE A:227 , ASP A:290 , GLY A:330 , ZN A:1411 , HOH A:2194 , HOH A:2270 , LEU B:78 , TYR B:79 , THR B:81 , ALA B:124 , HOH B:2155
BINDING SITE FOR RESIDUE TFG A1410
6
AC9
SOFTWARE
LEU A:78 , TYR A:79 , THR A:81 , ALA A:124 , PRO B:156 , HIS B:158 , HIS B:159 , GLY B:167 , PHE B:168 , ASP B:196 , HIS B:198 , PHE B:227 , ASP B:290 , GLY B:330 , ZN B:1410 , HOH B:2253 , HOH B:2338 , HOH B:2339
BINDING SITE FOR RESIDUE TFG B1409
7
BC2
SOFTWARE
ASP A:196 , HIS A:198 , ASP A:290 , TFG A:1410
BINDING SITE FOR RESIDUE ZN A1411
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SAPs(SNPs)/Variants
(1, 1)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_036042 (P83R, chain A, )
View:
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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
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(, 0)
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(0, 0)
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CATH Domains
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Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_Arb2_2vqqB01 (B:356-405)
1b: PFAM_Arb2_2vqqB02 (B:356-405)
2a: PFAM_Hist_deacetyl_2vqqB03 (B:20-349)
2b: PFAM_Hist_deacetyl_2vqqB04 (B:20-349)
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(
)
Clan
:
AB_hydrolase
(347)
Family
:
Arb2
(5)
Homo sapiens (Human)
(5)
1a
Arb2-2vqqB01
B:356-405
1b
Arb2-2vqqB02
B:356-405
Clan
:
Arginase
(56)
Family
:
Hist_deacetyl
(19)
Homo sapiens (Human)
(15)
2a
Hist_deacetyl-2vqqB03
B:20-349
2b
Hist_deacetyl-2vqqB04
B:20-349
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Chain A
Asymmetric Unit 1
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Asym.Unit (133 KB)
Header - Asym.Unit
Biol.Unit 1 (64 KB)
Header - Biol.Unit 1
Biol.Unit 2 (66 KB)
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