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3F07
Biol. Unit 1
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
(1, 1)
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:
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No.
Name
Count
Type
Full Name
1
AGE
1
Ligand/Ion
(2E)-N-HYDROXY-3-[1-METHYL-4-(PHENYLACETYL)-1H-PYRROL-2-YL]PROP-2-ENAMIDE
2
K
-1
Ligand/Ion
POTASSIUM ION
3
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:178 , HIS A:180 , ASP A:267 , AGE A:500
BINDING SITE FOR RESIDUE ZN A 400
2
AC2
SOFTWARE
ASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200
BINDING SITE FOR RESIDUE K A 401
3
AC3
SOFTWARE
PHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , SER A:226
BINDING SITE FOR RESIDUE K A 402
4
AC4
SOFTWARE
HIS A:78 , ASP A:87 , HIS A:90 , ASP A:92 , SER A:93
BINDING SITE FOR RESIDUE ZN A 409
5
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
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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
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Exons
(0, 0)
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Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
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SCOP Domains
(0, 0)
Info
All SCOP Domains
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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)
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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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Chain A
Asymmetric Unit 1
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Show PDB file:
Asym.Unit (178 KB)
Header - Asym.Unit
Biol.Unit 1 (61 KB)
Header - Biol.Unit 1
Biol.Unit 2 (62 KB)
Header - Biol.Unit 2
Biol.Unit 3 (57 KB)
Header - Biol.Unit 3
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