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3EWF
Asym. Unit
Info
Asym.Unit (247 KB)
Biol.Unit 1 (238 KB)
Biol.Unit 2 (64 KB)
Biol.Unit 3 (64 KB)
Biol.Unit 4 (63 KB)
Biol.Unit 5 (63 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF HUMAN HDAC8 H143A VARIANT COMPLEXED WITH SUBSTRATE.
Authors
:
D. P. Dowling, S. L. Gantt, S. G. Gattis, C. A. Fierke, D. W. Christianon
Date
:
14 Oct 08 (Deposition) - 30 Dec 08 (Release) - 30 Dec 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,C,D,I,J,K,L
Biol. Unit 1: A,B,C,D,I,J,K,L (1x)
Biol. Unit 2: A,I (1x)
Biol. Unit 3: B,J (1x)
Biol. Unit 4: C,K (1x)
Biol. Unit 5: D,L (1x)
Keywords
:
Hydrolase, Hdac, Metalloenzyme, Acetylation, Arginase Fold, Hdac8, Histone Deacetylase, Substrate Complex, 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
)
[
close entry info
]
Hetero Components
(5, 30)
Info
All Hetero Components
1a: ACETYL GROUP (ACEa)
1b: ACETYL GROUP (ACEb)
1c: ACETYL GROUP (ACEc)
1d: ACETYL GROUP (ACEd)
2a: N(6)-ACETYLLYSINE (ALYa)
2b: N(6)-ACETYLLYSINE (ALYb)
2c: N(6)-ACETYLLYSINE (ALYc)
2d: N(6)-ACETYLLYSINE (ALYd)
2e: N(6)-ACETYLLYSINE (ALYe)
2f: N(6)-ACETYLLYSINE (ALYf)
2g: N(6)-ACETYLLYSINE (ALYg)
2h: N(6)-ACETYLLYSINE (ALYh)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
3c: POTASSIUM ION (Kc)
3d: POTASSIUM ION (Kd)
3e: POTASSIUM ION (Ke)
3f: POTASSIUM ION (Kf)
3g: POTASSIUM ION (Kg)
3h: POTASSIUM ION (Kh)
4a: 7-AMINO-4-METHYL-CHROMEN-2-ONE (MCMa)
4b: 7-AMINO-4-METHYL-CHROMEN-2-ONE (MCMb)
4c: 7-AMINO-4-METHYL-CHROMEN-2-ONE (MCMc)
4d: 7-AMINO-4-METHYL-CHROMEN-2-ONE (MCMd)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
5d: ZINC ION (ZNd)
5e: ZINC ION (ZNe)
5f: ZINC ION (ZNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACE
4
Mod. Amino Acid
ACETYL GROUP
2
ALY
8
Mod. Amino Acid
N(6)-ACETYLLYSINE
3
K
8
Ligand/Ion
POTASSIUM ION
4
MCM
4
Ligand/Ion
7-AMINO-4-METHYL-CHROMEN-2-ONE
5
ZN
6
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(22, 22)
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)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
PHE C:191 , GLY C:220 , LYS C:221 , ARG I:2
BINDING SITE FOR RESIDUE ACE I 1
02
AC2
SOFTWARE
GLY A:341 , PRO A:342 , ARG J:2
BINDING SITE FOR RESIDUE ACE J 1
03
AC3
SOFTWARE
PHE A:191 , GLY A:220 , LYS A:221 , PRO D:342 , ARG K:2
BINDING SITE FOR RESIDUE ACE K 1
04
AC4
SOFTWARE
ARG L:2 , HIS L:3
BINDING SITE FOR RESIDUE ACE L 1
05
AC5
SOFTWARE
ASP A:178 , HIS A:180 , ASP A:267 , ALY I:5
BINDING SITE FOR RESIDUE ZN A 400
06
AC6
SOFTWARE
ASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200
BINDING SITE FOR RESIDUE K A 401
07
AC7
SOFTWARE
PHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , HOH A:802 , HOH A:803
BINDING SITE FOR RESIDUE K A 402
08
AC8
SOFTWARE
HIS A:375 , HOH A:920 , CYS D:352
BINDING SITE FOR RESIDUE ZN A 413
09
AC9
SOFTWARE
ASP B:178 , HIS B:180 , ASP B:267 , ALY J:5
BINDING SITE FOR RESIDUE ZN B 403
10
BC1
SOFTWARE
ASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200 , HIS B:201
BINDING SITE FOR RESIDUE K B 404
11
BC2
SOFTWARE
PHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , HOH B:801 , HOH B:901
BINDING SITE FOR RESIDUE K B 405
12
BC3
SOFTWARE
ASP C:178 , HIS C:180 , ASP C:267 , ALY K:5
BINDING SITE FOR RESIDUE ZN C 406
13
BC4
SOFTWARE
ASP C:176 , ASP C:178 , HIS C:180 , SER C:199 , LEU C:200
BINDING SITE FOR RESIDUE K C 407
14
BC5
SOFTWARE
PHE C:189 , THR C:192 , VAL C:195 , TYR C:225 , HOH C:806 , HOH C:820
BINDING SITE FOR RESIDUE K C 408
15
BC6
SOFTWARE
CYS B:352 , HOH B:891 , HIS C:375 , HOH C:1095
BINDING SITE FOR RESIDUE ZN C 412
16
BC7
SOFTWARE
ASP D:178 , HIS D:180 , ASP D:267 , ALY L:5
BINDING SITE FOR RESIDUE ZN D 409
17
BC8
SOFTWARE
ASP D:176 , ASP D:178 , HIS D:180 , SER D:199 , LEU D:200
BINDING SITE FOR RESIDUE K D 410
18
BC9
SOFTWARE
PHE D:189 , THR D:192 , VAL D:195 , TYR D:225 , HOH D:800
BINDING SITE FOR RESIDUE K D 411
19
CC1
SOFTWARE
LYS A:33 , TYR A:100 , ASP A:101 , PHE A:152 , LYS B:33 , PHE B:152 , PRO B:273 , ALY I:4 , ALY I:5
BINDING SITE FOR RESIDUE MCM I 6
20
CC2
SOFTWARE
LYS A:33 , PHE A:152 , PRO A:273 , LYS B:33 , TYR B:100 , ASP B:101 , PHE B:152 , ALY J:4 , ALY J:5
BINDING SITE FOR RESIDUE MCM J 6
21
CC3
SOFTWARE
LYS C:33 , TYR C:100 , ASP C:101 , PHE C:152 , LYS D:33 , PRO D:273 , ALY K:4 , ALY K:5 , MCM L:6
BINDING SITE FOR RESIDUE MCM K 6
22
CC4
SOFTWARE
LYS C:33 , PHE C:152 , PRO C:273 , LYS D:33 , TYR D:100 , ASP D:101 , PHE D:152 , MCM K:6 , ALY L:4 , ALY L:5
BINDING SITE FOR RESIDUE MCM L 6
[
close Site info
]
SAPs(SNPs)/Variants
(4, 16)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_069140 (H180R, chain A/B/C/D, )
2: VAR_069141 (T311M, chain A/B/C/D, )
3: VAR_069142 (G320R, chain A/B/C/D, )
4: VAR_069143 (H334R, chain A/B/C/D, )
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/D
H
180
R
2
UniProt
VAR_069141
T
311
M
HDAC8_HUMAN
Disease (CDLS5)
---
A/B/C/D
T
311
M
3
UniProt
VAR_069142
G
320
R
HDAC8_HUMAN
Disease (CDLS5)
---
A/B/C/D
G
320
R
4
UniProt
VAR_069143
H
334
R
HDAC8_HUMAN
Disease (CDLS5)
---
A/B/C/D
H
334
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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]
Exons
(11, 44)
Info
All Exons
Exon 1.1a (A:14-37 | B:14-37 | C:14-37 | D:14...)
Exon 1.3a (A:38-55 | B:38-55 | C:38-55 | D:38...)
Exon 1.4a (A:55-99 | B:55-99 | C:55-99 | D:55...)
Exon 1.5a (A:99-146 | B:99-146 | C:99-146 | D...)
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:371-377 ...)
View:
Select:
Label:
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
4
A:14-37
B:14-37
C:14-37
D:14-37
24
24
24
24
1.3a
ENST00000373573
3a
ENSE00001647366
X:71791959-71791907
53
HDAC8_HUMAN
38-55
18
4
A:38-55
B:38-55
C:38-55
D:38-55
18
18
18
18
1.4a
ENST00000373573
4a
ENSE00000978735
X:71788734-71788604
131
HDAC8_HUMAN
55-99
45
4
A:55-99
B:55-99
C:55-99
D:55-99
45
45
45
45
1.5a
ENST00000373573
5a
ENSE00001800363
X:71787880-71787739
142
HDAC8_HUMAN
99-146
48
4
A:99-146
B:99-146
C:99-146
D:99-146
48
48
48
48
1.6b
ENST00000373573
6b
ENSE00001682124
X:71715118-71715006
113
HDAC8_HUMAN
146-184
39
4
A:146-184
B:146-184
C:146-184
D:146-184
39
39
39
39
1.7b
ENST00000373573
7b
ENSE00001702232
X:71710856-71710779
78
HDAC8_HUMAN
184-210
27
4
A:184-210
B:184-210
C:184-210
D:184-210
27
27
27
27
1.9a
ENST00000373573
9a
ENSE00001682340
X:71708891-71708783
109
HDAC8_HUMAN
210-246
37
4
A:210-246
B:210-246
C:210-246
D:210-246
37
37
37
37
1.13b
ENST00000373573
13b
ENSE00001694695
X:71684581-71684409
173
HDAC8_HUMAN
246-304
59
4
A:246-304
B:246-304
C:246-304
D:246-304
59
59
59
59
1.15c
ENST00000373573
15c
ENSE00001436112
X:71681948-71681854
95
HDAC8_HUMAN
304-335
32
4
A:304-335
B:304-335
C:304-335
D:304-335
32
32
32
32
1.16b
ENST00000373573
16b
ENSE00001435962
X:71571688-71571583
106
HDAC8_HUMAN
336-371
36
4
A:336-371
B:336-371
C:336-371
D:336-371
36
36
36
36
1.18b
ENST00000373573
18b
ENSE00001859665
X:71549926-71549366
561
HDAC8_HUMAN
371-377
7
4
A:371-377
B:371-377
C:371-377
D:371-377
7
7
7
7
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3ewfa_ (A:)
1b: SCOP_d3ewfb_ (B:)
1c: SCOP_d3ewfc_ (C:)
1d: SCOP_d3ewfd_ (D:)
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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
:
automated matches
(15)
Human (Homo sapiens) [TaxId: 9606]
(15)
1a
d3ewfa_
A:
1b
d3ewfb_
B:
1c
d3ewfc_
C:
1d
d3ewfd_
D:
[
close SCOP info
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CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3ewfA00 (A:14-377)
1b: CATH_3ewfB00 (B:14-377)
1c: CATH_3ewfC00 (C:14-377)
1d: CATH_3ewfD00 (D: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
3ewfA00
A:14-377
1b
3ewfB00
B:14-377
1c
3ewfC00
C:14-377
1d
3ewfD00
D:14-377
[
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]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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Atom Selection
(currently selected atoms:
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