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1W22
Biol. Unit 2
Info
Asym.Unit (125 KB)
Biol.Unit 1 (62 KB)
Biol.Unit 2 (61 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF INHIBITED HUMAN HDAC8
Authors
:
A. Vannini, C. Volpari, E. Caroli Casavola, S. Di Marco
Date
:
25 Jun 04 (Deposition) - 24 Sep 04 (Release) - 30 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Hydroxamic Acid, Chromatin, Deacetylation, Hdac, Hydrolase, Nuclear Protein, Repressor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Vannini, C. Volpari, G. Filocamo, E. Caroli Casavola, M. Brunetti, D. Renzoni, P. Chakravarty, C. Paolini, R. De Francesco, P. Gallinari, C. Steinckuhler, S. Di Marco
Crystal Structure Of A Eukaryotic Zn-Dependent Histone Deacetylase, Human Hdac8, Complexed With A Hydroxamic Acid Inhibitor
Proc. Natl. Acad. Sci. Usa V. 101 15064 2004
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
2a: N-HYDROXY-4-(METHYL{[5-(2-PYRIDINY... (NHBa)
2b: N-HYDROXY-4-(METHYL{[5-(2-PYRIDINY... (NHBb)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
NHB
1
Ligand/Ion
N-HYDROXY-4-(METHYL{[5-(2-PYRIDINYL)-2-THIENYL]SULFONYL}AMINO)BENZAMIDE
3
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(5, 5)
Info
All Sites
1: AC4 (SOFTWARE)
2: AC5 (SOFTWARE)
3: AC6 (SOFTWARE)
4: AC7 (SOFTWARE)
5: AC8 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC4
SOFTWARE
ASP B:178 , HIS B:180 , ASP B:267 , NHB B:1378
BINDING SITE FOR RESIDUE ZN B1375
2
AC5
SOFTWARE
ASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200 , HIS B:201
BINDING SITE FOR RESIDUE K B1376
3
AC6
SOFTWARE
PHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , HOH B:2060
BINDING SITE FOR RESIDUE K B1377
4
AC7
SOFTWARE
ASP A:101 , HIS A:142 , HIS A:143 , GLY A:151 , PHE A:152 , ASP A:178 , HIS A:180 , PHE A:208 , ASP A:267 , GLY A:304 , TYR A:306 , ZN A:1375 , HOH A:2009 , HOH A:2154 , LYS B:33 , PRO B:273 , TYR B:306
BINDING SITE FOR RESIDUE NHB A1378
5
AC8
SOFTWARE
LYS A:33 , PHE A:152 , PRO A:273 , ASP B:101 , HIS B:142 , HIS B:143 , GLY B:151 , PHE B:152 , ASP B:178 , HIS B:180 , PHE B:208 , ASP B:267 , TYR B:306 , ZN B:1375 , HOH B:2058
BINDING SITE FOR RESIDUE NHB B1378
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_069140 (H180R, chain B, )
2: VAR_069141 (T311M, chain B, )
3: VAR_069142 (G320R, chain B, )
4: VAR_069143 (H334R, chain B, )
View:
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dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_069140
H
180
R
HDAC8_HUMAN
Disease (CDLS5)
---
B
H
180
R
2
UniProt
VAR_069141
T
311
M
HDAC8_HUMAN
Disease (CDLS5)
---
B
T
311
M
3
UniProt
VAR_069142
G
320
R
HDAC8_HUMAN
Disease (CDLS5)
---
B
G
320
R
4
UniProt
VAR_069143
H
334
R
HDAC8_HUMAN
Disease (CDLS5)
---
B
H
334
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(, 0)
Info
All PROSITE Patterns/Profiles
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Exons
(0, 0)
Info
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1w22a_ (A:)
1b: SCOP_d1w22b_ (B:)
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(
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Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Arginase/deacetylase
(138)
Superfamily
:
Arginase/deacetylase
(138)
Family
:
Histone deacetylase, HDAC
(28)
Protein domain
:
Histone deacetylase 8, HDAC8
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d1w22a_
A:
1b
d1w22b_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1w22A00 (A:13-375)
1b: CATH_1w22B00 (B:15-375)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Arginase; Chain A
(84)
Homologous Superfamily
:
[code=3.40.800.20, no name defined]
(21)
Homo sapiens. Organism_taxid: 9606.
(1)
1a
1w22A00
A:13-375
1b
1w22B00
B:15-375
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Hist_deacetyl_1w22B01 (B:21-323)
1b: PFAM_Hist_deacetyl_1w22B02 (B:21-323)
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Clans
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Organisms
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(
)
Clan
:
Arginase
(56)
Family
:
Hist_deacetyl
(19)
Homo sapiens (Human)
(15)
1a
Hist_deacetyl-1w22B01
B:21-323
1b
Hist_deacetyl-1w22B02
B:21-323
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Chain B
Asymmetric Unit 1
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