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1T67
Asym. Unit
Info
Asym.Unit (66 KB)
Biol.Unit 1 (59 KB)
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Title
:
CRYSTAL STRUCTURE OF HUMAN HDAC8 COMPLEXED WITH MS-344
Authors
:
J. R. Somoza, R. J. Skene, B. A. Katz, C. Mol, J. D. Ho, A. J. Jennings, C. Lu A. Arvai, J. J. Buggy, E. Chi, J. Tang, B. -C. Sang, E. Verner, R. Wynands E. M. Leahy, D. R. Dougan, G. Snell, M. Navre, M. W. Knuth, R. V. Swanson, D. E. Mcree, L. W. Tari
Date
:
05 May 04 (Deposition) - 27 Jul 04 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.31
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Histone Deacetylase, Zinc Hydrolase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. R. Somoza, R. J. Skene, B. A. Katz, C. Mol, J. D. Ho, A. J. Jennings, C. Luong, A. Arvai, J. J. Buggy, E. Chi, J. Tang, B. -C. Sang, E. Verner, R. Wynands, E. M. Leahy, D. R. Dougan, G. Snell, M. Navre, M. W. Knuth, R. V. Swanson, D. E. Mcree, L. W. Tari
Structural Snapshots Of Human Hdac8 Provide Insights Into The Class I Histone Deacetylases
Structure V. 12 1325 2004
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Hetero Components
(3, 4)
Info
All Hetero Components
1a: 4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMI... (B3Na)
2a: SODIUM ION (NAa)
2b: SODIUM ION (NAb)
3a: ZINC ION (ZNa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B3N
1
Ligand/Ion
4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2
NA
2
Ligand/Ion
SODIUM ION
3
ZN
1
Ligand/Ion
ZINC ION
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Sites
(4, 4)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:178 , HIS A:180 , ASP A:267 , B3N A:381
BINDING SITE FOR RESIDUE ZN A 378
2
AC2
SOFTWARE
ASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200
BINDING SITE FOR RESIDUE NA A 379
3
AC3
SOFTWARE
PHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , HOH A:480
BINDING SITE FOR RESIDUE NA A 380
4
AC4
SOFTWARE
LYS A:33 , TYR A:100 , HIS A:142 , HIS A:143 , GLY A:151 , PHE A:152 , ASP A:178 , HIS A:180 , PHE A:208 , ASP A:267 , PRO A:273 , MET A:274 , GLY A:304 , TYR A:306 , ZN A:378 , HOH A:392
BINDING SITE FOR RESIDUE B3N A 381
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SAPs(SNPs)/Variants
(4, 4)
Info
(mutated residues are not available)
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:
Select:
Label:
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, 0)
Info
All PROSITE Patterns/Profiles
;
View:
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End label:
Sorry, no Info available
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Exons
(11, 11)
Info
All Exons
Exon 1.1a (A:14-37)
Exon 1.3a (A:38-55)
Exon 1.4a (A:55-99 (gaps))
Exon 1.5a (A:99-146)
Exon 1.6b (A:146-184)
Exon 1.7b (A:184-210)
Exon 1.9a (A:210-246)
Exon 1.13b (A:246-304)
Exon 1.15c (A:304-335)
Exon 1.16b (A:336-371)
Exon 1.18b (A:371-377)
View:
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All Exon Boundaries
01: Boundary -/1.1a
02: Boundary 1.1a/1.3a
03: Boundary 1.3a/1.4a
04: Boundary 1.4a/1.5a
05: Boundary 1.5a/1.6b
06: Boundary 1.6b/1.7b
07: Boundary 1.7b/1.9a
08: Boundary 1.9a/1.13b
09: Boundary 1.13b/1.15c
10: Boundary 1.15c/1.16b
11: Boundary 1.16b/1.18b
12: Boundary 1.18b/-
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
ENST00000373573
1a
ENSE00001889063
X:71792953-71792501
453
HDAC8_HUMAN
1-37
37
1
A:14-37
24
1.3a
ENST00000373573
3a
ENSE00001647366
X:71791959-71791907
53
HDAC8_HUMAN
38-55
18
1
A:38-55
18
1.4a
ENST00000373573
4a
ENSE00000978735
X:71788734-71788604
131
HDAC8_HUMAN
55-99
45
1
A:55-99 (gaps)
45
1.5a
ENST00000373573
5a
ENSE00001800363
X:71787880-71787739
142
HDAC8_HUMAN
99-146
48
1
A:99-146
48
1.6b
ENST00000373573
6b
ENSE00001682124
X:71715118-71715006
113
HDAC8_HUMAN
146-184
39
1
A:146-184
39
1.7b
ENST00000373573
7b
ENSE00001702232
X:71710856-71710779
78
HDAC8_HUMAN
184-210
27
1
A:184-210
27
1.9a
ENST00000373573
9a
ENSE00001682340
X:71708891-71708783
109
HDAC8_HUMAN
210-246
37
1
A:210-246
37
1.13b
ENST00000373573
13b
ENSE00001694695
X:71684581-71684409
173
HDAC8_HUMAN
246-304
59
1
A:246-304
59
1.15c
ENST00000373573
15c
ENSE00001436112
X:71681948-71681854
95
HDAC8_HUMAN
304-335
32
1
A:304-335
32
1.16b
ENST00000373573
16b
ENSE00001435962
X:71571688-71571583
106
HDAC8_HUMAN
336-371
36
1
A:336-371
36
1.18b
ENST00000373573
18b
ENSE00001859665
X:71549926-71549366
561
HDAC8_HUMAN
371-377
7
1
A:371-377
7
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SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1t67a_ (A:)
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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
d1t67a_
A:
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CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1t67A00 (A:14-377)
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Homologous Superfamilies
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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
1t67A00
A:14-377
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Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Hist_deacetyl_1t67A01 (A:21-323)
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Clans
(
)
(
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Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Arginase
(56)
Family
:
Hist_deacetyl
(19)
Homo sapiens (Human)
(15)
1a
Hist_deacetyl-1t67A01
A:21-323
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Asymmetric Unit 1
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