PLEASE WAIT...
Getting 'Biological Unit' information from database.
PLEASE WAIT...
Getting 'Hetero Component' information from database.
PLEASE WAIT...
Getting 'Site' information from database.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
2V5X
Asym. Unit
Info
Asym.Unit (130 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (63 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(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:
[
Gene Ontology, PubMed, Web (Google)
]
)
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
[
close entry info
]
Hetero Components
(3, 8)
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:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
4
Ligand/Ion
POTASSIUM ION
2
V5X
2
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
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
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
AC2
SOFTWARE
ASP B:178 , HIS B:180 , ASP B:267 , V5X B:1380
BINDING SITE FOR RESIDUE ZN B1377
3
AC3
SOFTWARE
ASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200
BINDING SITE FOR RESIDUE K A1378
4
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
5
AC5
SOFTWARE
ASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200
BINDING SITE FOR RESIDUE K B1378
6
AC6
SOFTWARE
PHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , HOH B:2069 , HOH B:2092
BINDING SITE FOR RESIDUE K B1379
7
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
8
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
[
close Site info
]
SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_069140 (H180R, chain A/B, )
2: VAR_069141 (T311M, chain A/B, )
3: VAR_069142 (G320R, chain A/B, )
4: VAR_069143 (H334R, chain A/B, )
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
H
180
R
2
UniProt
VAR_069141
T
311
M
HDAC8_HUMAN
Disease (CDLS5)
---
A/B
T
311
M
3
UniProt
VAR_069142
G
320
R
HDAC8_HUMAN
Disease (CDLS5)
---
A/B
G
320
R
4
UniProt
VAR_069143
H
334
R
HDAC8_HUMAN
Disease (CDLS5)
---
A/B
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
[
close PROSITE info
]
Exons
(11, 22)
Info
All Exons
Exon 1.1a (A:14-37 | B:14-37)
Exon 1.3a (A:38-55 | B:38-55)
Exon 1.4a (A:55-99 | B:55-99 (gaps))
Exon 1.5a (A:99-146 | B:99-146)
Exon 1.6b (A:146-184 | B:146-184)
Exon 1.7b (A:184-210 | B:184-210)
Exon 1.9a (A:210-246 | B:210-246)
Exon 1.13b (A:246-304 | B:246-304)
Exon 1.15c (A:304-335 | B:304-335)
Exon 1.16b (A:336-371 | B:336-371)
Exon 1.18b (A:371-376 | B:371-376)
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
2
A:14-37
B:14-37
24
24
1.3a
ENST00000373573
3a
ENSE00001647366
X:71791959-71791907
53
HDAC8_HUMAN
38-55
18
2
A:38-55
B:38-55
18
18
1.4a
ENST00000373573
4a
ENSE00000978735
X:71788734-71788604
131
HDAC8_HUMAN
55-99
45
2
A:55-99
B:55-99 (gaps)
45
45
1.5a
ENST00000373573
5a
ENSE00001800363
X:71787880-71787739
142
HDAC8_HUMAN
99-146
48
2
A:99-146
B:99-146
48
48
1.6b
ENST00000373573
6b
ENSE00001682124
X:71715118-71715006
113
HDAC8_HUMAN
146-184
39
2
A:146-184
B:146-184
39
39
1.7b
ENST00000373573
7b
ENSE00001702232
X:71710856-71710779
78
HDAC8_HUMAN
184-210
27
2
A:184-210
B:184-210
27
27
1.9a
ENST00000373573
9a
ENSE00001682340
X:71708891-71708783
109
HDAC8_HUMAN
210-246
37
2
A:210-246
B:210-246
37
37
1.13b
ENST00000373573
13b
ENSE00001694695
X:71684581-71684409
173
HDAC8_HUMAN
246-304
59
2
A:246-304
B:246-304
59
59
1.15c
ENST00000373573
15c
ENSE00001436112
X:71681948-71681854
95
HDAC8_HUMAN
304-335
32
2
A:304-335
B:304-335
32
32
1.16b
ENST00000373573
16b
ENSE00001435962
X:71571688-71571583
106
HDAC8_HUMAN
336-371
36
2
A:336-371
B:336-371
36
36
1.18b
ENST00000373573
18b
ENSE00001859665
X:71549926-71549366
561
HDAC8_HUMAN
371-377
7
2
A:371-376
B:371-376
6
6
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d2v5xa_ (A:)
1b: SCOP_d2v5xb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
d2v5xa_
A:
1b
d2v5xb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_2v5xA00 (A:14-376)
1b: CATH_2v5xB00 (B:14-376)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
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
2v5xA00
A:14-376
1b
2v5xB00
B:14-376
[
close CATH info
]
Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Hist_deacetyl_2v5xB01 (B:21-323)
1b: PFAM_Hist_deacetyl_2v5xB02 (B:21-323)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
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
[
close Pfam info
]
Atom Selection
(currently selected atoms:
all
)
Protein
Nucleic
Backbone
Sidechain
Hetero
Ligand
Solvent
All Atoms
Protein & NOT Variant
Protein & NOT Site
Protein & NOT PROSITE
Chain A
Chain B
Asymmetric Unit 1
Rendering
(selected part)
Molecule Coloring
(selected part)
by Chain (Asym. Unit)
by Chain (Biol. Unit)
by Secondary Structure
by Atom (CPK)
by SCOP Domain
by CATH Domain
by Pfam Domain
by Asymmetric Unit
by Exon
by Amino Acid
by Nucleotide
by Temperature
by Charge
by Rainbow (Group)
by Custom Color
Background Coloring
Choose
molecule
background
color...
[
close
]
RGB value
(e.g.: "#3cb371" or "60,179,113")
Stereo
Graphics Window
x
pixel
Miscellaneous
Script
Example Commands
Example Command
Action
select :A, :C
select chains 'A' and 'C'
select [ALA]:A
select all 'ALA' residues (Alanines) in chain 'A'
select 5-10
select residue range 5 to 10 in all chains
select 5-10:A
select residue range 5 to 10 in chain 'A'
select protein & not helix & not sheet
select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
ssbonds 100
show SS bonds with a radius of 100 units (=0.4Å)
wireframe 100
show bonds with a radius of 100 units (=0.4Å)
[
close Script example commands
]
Log
Note:
In this "Basic Interface" any change in the selection of a pulldown menu automatically triggers an action (one-step mechanism).
View and selection are coupled in the structure specific controls (e.g. "Hetero","PROSITE") .
Note:
In this "Advanced Interface" any change in the selection of a pulldown menu only sets the target for the corresponding control buttons (two-step mechanism).
View and selection are set independently in the structure specific controls (e.g. "Hetero","PROSITE") .
QuickSearch:
by PDB,NDB,UniProt,PROSITE Code or
Search Term(s)
Show PDB file:
Asym.Unit (130 KB)
Header - Asym.Unit
Biol.Unit 1 (64 KB)
Header - Biol.Unit 1
Biol.Unit 2 (63 KB)
Header - Biol.Unit 2
Plain Text
HTML (compressed size)
use JSmol [Javascript]
use Jmol [Java applet]
Upload:
Select a local file
OR
Enter a remote file address
You can upload any molecular structure file format that is recognized by Jmol,
e.g.: PDB, mmCif, CIF, CML, MOL, XYZ
(also compressed with 'gzip', see the
Jmol documentation
for a complete list)
JenaLib Atlas Page
|
Sequence/Alignment View
2V5X
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help