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3F0R
Biol. Unit 3
Info
Asym.Unit (184 KB)
Biol.Unit 1 (63 KB)
Biol.Unit 2 (63 KB)
Biol.Unit 3 (61 KB)
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(1)
Title
:
CRYSTAL STRUCTURE ANALYSIS OF HUMAN HDAC8 COMPLEXED WITH TRICHOSTATIN A IN A NEW MONOCLINIC CRYSTAL FORM
Authors
:
D. P. Dowling, S. L. Gantt, S. G. Gattis, C. A. Fierke, D. W. Christianson
Date
:
25 Oct 08 (Deposition) - 30 Dec 08 (Release) - 30 Dec 08 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.54
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, 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
(1, 2)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
1e: POTASSIUM ION (Ke)
1f: POTASSIUM ION (Kf)
2a: TRICHOSTATIN A (TSNa)
2b: TRICHOSTATIN A (TSNb)
2c: TRICHOSTATIN A (TSNc)
2d: TRICHOSTATIN A (TSNd)
2e: TRICHOSTATIN A (TSNe)
2f: TRICHOSTATIN A (TSNf)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
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Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
TSN
2
Ligand/Ion
TRICHOSTATIN A
3
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(5, 5)
Info
All Sites
1: BC2 (SOFTWARE)
2: BC3 (SOFTWARE)
3: BC4 (SOFTWARE)
4: BC5 (SOFTWARE)
5: BC6 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
BC2
SOFTWARE
ASP C:178 , HIS C:180 , ASP C:267 , TSN C:802
BINDING SITE FOR RESIDUE ZN C 406
2
BC3
SOFTWARE
PHE C:189 , THR C:192 , VAL C:195 , TYR C:225 , HOH C:392
BINDING SITE FOR RESIDUE K C 407
3
BC4
SOFTWARE
ASP C:176 , ASP C:178 , HIS C:180 , SER C:199 , LEU C:200 , HIS C:201
BINDING SITE FOR RESIDUE K C 408
4
BC5
SOFTWARE
LYS C:33 , TYR C:100 , HIS C:142 , HIS C:143 , PHE C:152 , ASP C:178 , HIS C:180 , ASP C:267 , TYR C:306 , ZN C:406 , TSN C:803
BINDING SITE FOR RESIDUE TSN C 802
5
BC6
SOFTWARE
LYS C:33 , PRO C:35 , ARG C:37 , TYR C:111 , TRP C:141 , PRO C:273 , MET C:274 , TYR C:306 , TSN C:802
BINDING SITE FOR RESIDUE TSN C 803
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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 C, )
2: VAR_069141 (T311M, chain C, )
3: VAR_069142 (G320R, chain C, )
4: VAR_069143 (H334R, chain C, )
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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)
---
C
H
180
R
2
UniProt
VAR_069141
T
311
M
HDAC8_HUMAN
Disease (CDLS5)
---
C
T
311
M
3
UniProt
VAR_069142
G
320
R
HDAC8_HUMAN
Disease (CDLS5)
---
C
G
320
R
4
UniProt
VAR_069143
H
334
R
HDAC8_HUMAN
Disease (CDLS5)
---
C
H
334
R
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
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PROSITE Patterns/Profiles
(, 0)
Info
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Exons
(0, 0)
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All Exons
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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, 3)
Info
All SCOP Domains
1a: SCOP_d3f0ra_ (A:)
1b: SCOP_d3f0rb_ (B:)
1c: SCOP_d3f0rc_ (C:)
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Protein Domains
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Organisms
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(
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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
d3f0ra_
A:
1b
d3f0rb_
B:
1c
d3f0rc_
C:
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CATH Domains
(1, 3)
Info
all CATH domains
1a: CATH_3f0rA00 (A:13-378)
1b: CATH_3f0rB00 (B:13-378)
1c: CATH_3f0rC00 (C:13-377)
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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
3f0rA00
A:13-378
1b
3f0rB00
B:13-378
1c
3f0rC00
C:13-377
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Pfam Domains
(0, 0)
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Chain C
Asymmetric Unit 1
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Asym.Unit (184 KB)
Header - Asym.Unit
Biol.Unit 1 (63 KB)
Header - Biol.Unit 1
Biol.Unit 2 (63 KB)
Header - Biol.Unit 2
Biol.Unit 3 (61 KB)
Header - Biol.Unit 3
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