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3F07
Asym. Unit
Info
Asym.Unit (178 KB)
Biol.Unit 1 (61 KB)
Biol.Unit 2 (62 KB)
Biol.Unit 3 (57 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF HUMAN HDAC8 COMPLEXED WITH APHA IN A NEW MONOCLINIC CRYSTAL FORM
Authors
:
D. P. Dowling, S. L. Gantt, S. G. Gattis, C. A. Fierke, D. W. Christianson
Date
:
24 Oct 08 (Deposition) - 30 Dec 08 (Release) - 30 Dec 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Hydrolase, Hdac, Metalloenzyme, Acetylation, Arginase Fold, Hdac8, Histone Deacetylase 8 , Hydroxamate Inhibitor, Mutant, Alternative Splicing, Chromatin Regulator, Nucleus, Repressor, Transcription, Transcription Regulation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. P. Dowling, S. L. Gantt, S. G. Gattis, C. A. Fierke, D. W. Christianson
Structural Studies Of Human Histone Deacetylase 8 And Its Site-Specific Variants Complexed With Substrate And Inhibitors.
Biochemistry V. 47 13554 2008
(for further references see the
PDB file header
)
[
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Hetero Components
(3, 12)
Info
All Hetero Components
1a: (2E)-N-HYDROXY-3-[1-METHYL-4-(PHEN... (AGEa)
1b: (2E)-N-HYDROXY-3-[1-METHYL-4-(PHEN... (AGEb)
2a: POTASSIUM ION (Ka)
2b: POTASSIUM ION (Kb)
2c: POTASSIUM ION (Kc)
2d: POTASSIUM ION (Kd)
2e: POTASSIUM ION (Ke)
2f: POTASSIUM ION (Kf)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AGE
2
Ligand/Ion
(2E)-N-HYDROXY-3-[1-METHYL-4-(PHENYLACETYL)-1H-PYRROL-2-YL]PROP-2-ENAMIDE
2
K
6
Ligand/Ion
POTASSIUM ION
3
ZN
4
Ligand/Ion
ZINC ION
[
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Sites
(12, 12)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:178 , HIS A:180 , ASP A:267 , AGE A:500
BINDING SITE FOR RESIDUE ZN A 400
02
AC2
SOFTWARE
ASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200
BINDING SITE FOR RESIDUE K A 401
03
AC3
SOFTWARE
PHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , SER A:226
BINDING SITE FOR RESIDUE K A 402
04
AC4
SOFTWARE
HIS A:78 , ASP A:87 , HIS A:90 , ASP A:92 , SER A:93
BINDING SITE FOR RESIDUE ZN A 409
05
AC5
SOFTWARE
LYS A:33 , ASP A:101 , HIS A:142 , HIS A:143 , ASP A:178 , HIS A:180 , GLY A:206 , PHE A:208 , ASP A:267 , MET A:274 , TYR A:306 , ZN A:400
BINDING SITE FOR RESIDUE AGE A 500
06
AC6
SOFTWARE
ASP B:178 , HIS B:180 , ASP B:267 , AGE B:501
BINDING SITE FOR RESIDUE ZN B 403
07
AC7
SOFTWARE
ASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200
BINDING SITE FOR RESIDUE K B 404
08
AC8
SOFTWARE
PHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , SER B:226
BINDING SITE FOR RESIDUE K B 405
09
AC9
SOFTWARE
LYS B:33 , ASP B:101 , HIS B:142 , HIS B:143 , PHE B:152 , ASP B:178 , HIS B:180 , PHE B:207 , PHE B:208 , MET B:274 , GLY B:304 , TYR B:306 , ZN B:403
BINDING SITE FOR RESIDUE AGE B 501
10
BC1
SOFTWARE
ASP C:178 , HIS C:180 , ASP C:267 , HOH C:813
BINDING SITE FOR RESIDUE ZN C 406
11
BC2
SOFTWARE
ASP C:176 , ASP C:178 , HIS C:180 , SER C:199 , LEU C:200
BINDING SITE FOR RESIDUE K C 407
12
BC3
SOFTWARE
PHE C:189 , THR C:192 , VAL C:195 , TYR C:225 , SER C:226
BINDING SITE FOR RESIDUE K C 408
[
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]
SAPs(SNPs)/Variants
(4, 12)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_069140 (H180R, chain A/B/C, )
2: VAR_069141 (T311M, chain A/B/C, )
3: VAR_069142 (G320R, chain A/B/C, )
4: VAR_069143 (H334R, chain A/B/C, )
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/B/C
H
180
R
2
UniProt
VAR_069141
T
311
M
HDAC8_HUMAN
Disease (CDLS5)
---
A/B/C
T
311
M
3
UniProt
VAR_069142
G
320
R
HDAC8_HUMAN
Disease (CDLS5)
---
A/B/C
G
320
R
4
UniProt
VAR_069143
H
334
R
HDAC8_HUMAN
Disease (CDLS5)
---
A/B/C
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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Label:
End label:
Sorry, no Info available
[
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]
Exons
(11, 33)
Info
All Exons
Exon 1.1a (A:13-37 | B:13-37 | C:13-37)
Exon 1.3a (A:38-55 | B:38-55 | C:38-55)
Exon 1.4a (A:55-99 | B:55-99 | C:55-83)
Exon 1.5a (A:99-146 | B:99-146 | C:108-146)
Exon 1.6b (A:146-184 | B:146-184 | C:146-184)
Exon 1.7b (A:184-210 | B:184-210 | C:184-210)
Exon 1.9a (A:210-246 | B:210-246 | C:210-246)
Exon 1.13b (A:246-304 | B:246-304 | C:246-304)
Exon 1.15c (A:304-335 | B:304-335 | C:304-335)
Exon 1.16b (A:336-371 | B:336-371 | C:336-371)
Exon 1.18b (A:371-377 | B:371-377 | C:371-376)
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
3
A:13-37
B:13-37
C:13-37
25
25
25
1.3a
ENST00000373573
3a
ENSE00001647366
X:71791959-71791907
53
HDAC8_HUMAN
38-55
18
3
A:38-55
B:38-55
C:38-55
18
18
18
1.4a
ENST00000373573
4a
ENSE00000978735
X:71788734-71788604
131
HDAC8_HUMAN
55-99
45
3
A:55-99
B:55-99
C:55-83
45
45
29
1.5a
ENST00000373573
5a
ENSE00001800363
X:71787880-71787739
142
HDAC8_HUMAN
99-146
48
3
A:99-146
B:99-146
C:108-146
48
48
39
1.6b
ENST00000373573
6b
ENSE00001682124
X:71715118-71715006
113
HDAC8_HUMAN
146-184
39
3
A:146-184
B:146-184
C:146-184
39
39
39
1.7b
ENST00000373573
7b
ENSE00001702232
X:71710856-71710779
78
HDAC8_HUMAN
184-210
27
3
A:184-210
B:184-210
C:184-210
27
27
27
1.9a
ENST00000373573
9a
ENSE00001682340
X:71708891-71708783
109
HDAC8_HUMAN
210-246
37
3
A:210-246
B:210-246
C:210-246
37
37
37
1.13b
ENST00000373573
13b
ENSE00001694695
X:71684581-71684409
173
HDAC8_HUMAN
246-304
59
3
A:246-304
B:246-304
C:246-304
59
59
59
1.15c
ENST00000373573
15c
ENSE00001436112
X:71681948-71681854
95
HDAC8_HUMAN
304-335
32
3
A:304-335
B:304-335
C:304-335
32
32
32
1.16b
ENST00000373573
16b
ENSE00001435962
X:71571688-71571583
106
HDAC8_HUMAN
336-371
36
3
A:336-371
B:336-371
C:336-371
36
36
36
1.18b
ENST00000373573
18b
ENSE00001859665
X:71549926-71549366
561
HDAC8_HUMAN
371-377
7
3
A:371-377
B:371-377
C:371-376
7
7
6
[
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]
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
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Sorry, no Info available
[
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_3f07A00 (A:13-378)
1b: CATH_3f07B00 (B:13-380)
1c: CATH_3f07C00 (C:13-376)
View:
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(
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(
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(
)
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(
)
(
)
Homologous Superfamilies
(
)
(
)
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
3f07A00
A:13-378
1b
3f07B00
B:13-380
1c
3f07C00
C:13-376
[
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Pfam Domains
(0, 0)
Info
all PFAM domains
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Sorry, no Info available
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