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3EZT
Biol. Unit 1
Info
Asym.Unit (124 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (60 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF HUMAN HDAC8 D101E VARIANT
Authors
:
D. P. Dowling, S. L. Gantt, S. G. Gattis, C. A. Fierke, D. W. Christianon
Date
:
23 Oct 08 (Deposition) - 30 Dec 08 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.85
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Hydrolase, Hdac, Metalloenzyme, Arginase Fold, Hdac8, Histone Deacetylase 8, Hydroxamate Inhibitor, Mutant, Chromatin Regulator, Nucleus, Repressor, Transcription, Transcription Regulation
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. P. Dowling, S. L. Gantt, S. G. Gattis, C. A. Fierke, D. W. Christianso
Structural Studies Of Human Histone Deacetylase 8 And Its Site-Specific Variants Complexed With Substrate And Inhibitors.
Biochemistry V. 47 13554 2008
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Hetero Components
(2, 2)
Info
All Hetero Components
1a: 4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMI... (B3Na)
1b: 4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMI... (B3Nb)
2a: BETA-MERCAPTOETHANOL (BMEa)
2b: BETA-MERCAPTOETHANOL (BMEb)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
3c: POTASSIUM ION (Kc)
3d: POTASSIUM ION (Kd)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
B3N
1
Ligand/Ion
4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2
BME
1
Ligand/Ion
BETA-MERCAPTOETHANOL
3
K
-1
Ligand/Ion
POTASSIUM ION
4
ZN
-1
Ligand/Ion
ZINC 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: AC9 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:178 , HIS A:180 , ASP A:267 , B3N A:500
BINDING SITE FOR RESIDUE ZN A 402
2
AC2
SOFTWARE
PHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , SER A:226 , HOH A:394
BINDING SITE FOR RESIDUE K A 403
3
AC3
SOFTWARE
ASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200 , HIS A:201
BINDING SITE FOR RESIDUE K A 404
4
AC4
SOFTWARE
TYR A:100 , HIS A:142 , HIS A:143 , ASP A:178 , HIS A:180 , PHE A:208 , ASP A:267 , GLY A:304 , TYR A:306 , ZN A:402 , LYS B:33 , PHE B:152 , PRO B:273 , TYR B:306 , B3N B:501
BINDING SITE FOR RESIDUE B3N A 500
5
AC5
SOFTWARE
TRP A:141 , GLY A:151
BINDING SITE FOR RESIDUE BME A 601
6
AC9
SOFTWARE
LYS A:33 , PHE A:152 , PRO A:273 , TYR A:306 , B3N A:500 , TYR B:100 , HIS B:142 , HIS B:143 , PHE B:152 , ASP B:178 , HIS B:180 , PHE B:208 , ASP B:267 , GLY B:304 , TYR B:306 , ZN B:401 , BME B:600
BINDING SITE FOR RESIDUE B3N B 501
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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 A, )
2: VAR_069141 (T311M, chain A, )
3: VAR_069142 (G320R, chain A, )
4: VAR_069143 (H334R, chain A, )
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)
---
A
H
180
R
2
UniProt
VAR_069141
T
311
M
HDAC8_HUMAN
Disease (CDLS5)
---
A
T
311
M
3
UniProt
VAR_069142
G
320
R
HDAC8_HUMAN
Disease (CDLS5)
---
A
G
320
R
4
UniProt
VAR_069143
H
334
R
HDAC8_HUMAN
Disease (CDLS5)
---
A
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_d3ezta_ (A:)
1b: SCOP_d3eztb_ (B:)
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Protein Domains
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(
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Organisms
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)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Arginase/deacetylase
(138)
Superfamily
:
Arginase/deacetylase
(138)
Family
:
Histone deacetylase, HDAC
(28)
Protein domain
:
automated matches
(15)
Human (Homo sapiens) [TaxId: 9606]
(15)
1a
d3ezta_
A:
1b
d3eztb_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_3eztA00 (A:14-377)
1b: CATH_3eztB00 (B:14-377)
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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)
Human (Homo sapiens)
(17)
1a
3eztA00
A:14-377
1b
3eztB00
B:14-377
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Pfam Domains
(0, 0)
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Chain A
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (124 KB)
Header - Asym.Unit
Biol.Unit 1 (61 KB)
Header - Biol.Unit 1
Biol.Unit 2 (60 KB)
Header - Biol.Unit 2
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