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2V5X
Biol. Unit 1
Info
Asym.Unit (130 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (63 KB)
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(1)
Title
:
CRYSTAL STRUCTURE OF HDAC8-INHIBITOR COMPLEX
Authors
:
S. Di Marco, A. Vannini, C. Volpari, P. Gallinari, P. Jones, M. Mattu, A R. Defrancesco, C. Steinkuhler
Date
:
10 Jul 07 (Deposition) - 04 Sep 07 (Release) - 12 Sep 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Hydroxamate Inhibitor, Chromatin Regulator, Histone Deacetylase, P53, Hdac, Hdac8, Nucleus, Hydrolase, Repressor, Chromatin, Drug Design, Deacetylation, Transcription, Transcription Regulation, Nuclear Protein, Peptidic Substrate
(Keyword Search:
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Gene Ontology, PubMed, Web (Google)
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Reference
:
A. Vannini, C. Volpari, P. Gallinari, P. Jones, M. Mattu, A. Carfi, R. Defrancesco, C. Steinkuhler, S. Di Marco
Substrate Binding To Histone Deacetylases As Revealed By Crystal Structure Of Hdac8-Substrate Complex
Embo Rep. V. 8 879 2007
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Hetero Components
(1, 1)
Info
All Hetero Components
1a: POTASSIUM ION (Ka)
1b: POTASSIUM ION (Kb)
1c: POTASSIUM ION (Kc)
1d: POTASSIUM ION (Kd)
2a: (2R)-N~8~-HYDROXY-2-{[(5-METHOXY-2... (V5Xa)
2b: (2R)-N~8~-HYDROXY-2-{[(5-METHOXY-2... (V5Xb)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
View:
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Label:
No.
Name
Count
Type
Full Name
1
K
-1
Ligand/Ion
POTASSIUM ION
2
V5X
1
Ligand/Ion
(2R)-N~8~-HYDROXY-2-{[(5-METHOXY-2-METHYL-1H-INDOL-3-YL)ACETYL]AMINO}-N~1~-[2-(2-PHENYL-1H-INDOL-3-YL)ETHYL]OCTANEDIAMIDE
3
ZN
-1
Ligand/Ion
ZINC ION
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Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC4 (SOFTWARE)
4: AC7 (SOFTWARE)
5: AC8 (SOFTWARE)
View:
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP A:178 , HIS A:180 , ASP A:267 , V5X A:1380
BINDING SITE FOR RESIDUE ZN A1377
2
AC3
SOFTWARE
ASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200
BINDING SITE FOR RESIDUE K A1378
3
AC4
SOFTWARE
PHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , HOH A:2064 , HOH A:2086
BINDING SITE FOR RESIDUE K A1379
4
AC7
SOFTWARE
ASP A:101 , HIS A:142 , HIS A:143 , GLY A:151 , ASP A:178 , HIS A:180 , PHE A:208 , PRO A:209 , ASP A:267 , PRO A:273 , MET A:274 , GLY A:304 , TYR A:306 , ZN A:1377 , HOH A:2076 , HOH A:2152 , PHE B:152 , PRO B:273 , MET B:274 , V5X B:1380
BINDING SITE FOR RESIDUE V5X A1380
5
AC8
SOFTWARE
LYS A:33 , PRO A:273 , TYR A:306 , V5X A:1380 , ASP B:101 , HIS B:142 , HIS B:143 , GLY B:151 , PHE B:152 , ASP B:178 , HIS B:180 , PHE B:208 , PRO B:209 , GLY B:210 , ASP B:267 , TYR B:306 , ZN B:1377 , HOH B:2168
BINDING SITE FOR RESIDUE V5X B1380
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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)
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Exons
(0, 0)
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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
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2v5xa_ (A:)
1b: SCOP_d2v5xb_ (B:)
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Protein Domains
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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
d2v5xa_
A:
1b
d2v5xb_
B:
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CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2v5xA00 (A:14-376)
1b: CATH_2v5xB00 (B:14-376)
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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
2v5xA00
A:14-376
1b
2v5xB00
B:14-376
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Hist_deacetyl_2v5xB01 (B:21-323)
1b: PFAM_Hist_deacetyl_2v5xB02 (B:21-323)
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Clan
:
Arginase
(56)
Family
:
Hist_deacetyl
(19)
Homo sapiens (Human)
(15)
1a
Hist_deacetyl-2v5xB01
B:21-323
1b
Hist_deacetyl-2v5xB02
B:21-323
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Chain A
Asymmetric Unit 1
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Asym.Unit (130 KB)
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Biol.Unit 1 (64 KB)
Header - Biol.Unit 1
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