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.
3RQD
Biol. Unit 3
Info
Asym.Unit (132 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (65 KB)
Biol.Unit 3 (125 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
IDEAL THIOLATE-ZINC COORDINATION GEOMETRY IN DEPSIPEPTIDE BINDING TO HISTONE DEACETYLASE 8
Authors
:
K. E Cole, D. P. Dowling, D. W. Christianson
Date
:
28 Apr 11 (Deposition) - 24 Aug 11 (Release) - 21 Mar 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.14
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Biol. Unit 3: A,B,C,D (1x)
Keywords
:
Histone Deacetylase, Largazole, Histone Deacetylation, Hydrolase- Hydrolase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. E. Cole, D. P. Dowling, M. A. Boone, A. J. Phillips, D. W. Christianso
Structural Basis Of The Antiproliferative Activity Of Largazole, A Depsipeptide Inhibitor Of The Histone Deacetylases.
J. Am. Chem. Soc. V. 133 12474 2011
[
close entry info
]
Hetero Components
(3, 6)
Info
All Hetero Components
1a: (3S,4E)-3-HYDROXY-7-SULFANYLHEPT-4... (02Ga)
1b: (3S,4E)-3-HYDROXY-7-SULFANYLHEPT-4... (02Gb)
2a: 2-METHYL-L-CYSTEINE (03Ya)
2b: 2-METHYL-L-CYSTEINE (03Yb)
3a: (2Z)-2-AMINO-3-SULFANYLPROP-2-ENOI... (BB9a)
3b: (2Z)-2-AMINO-3-SULFANYLPROP-2-ENOI... (BB9b)
4a: POTASSIUM ION (Ka)
4b: POTASSIUM ION (Kb)
4c: POTASSIUM ION (Kc)
4d: POTASSIUM ION (Kd)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
02G
2
Mod. Amino Acid
(3S,4E)-3-HYDROXY-7-SULFANYLHEPT-4-ENOIC ACID
2
03Y
2
Mod. Amino Acid
2-METHYL-L-CYSTEINE
3
BB9
2
Mod. Amino Acid
(2Z)-2-AMINO-3-SULFANYLPROP-2-ENOIC ACID
4
K
-1
Ligand/Ion
POTASSIUM ION
5
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASP B:178 , HIS B:180 , ASP B:267 , 02G D:1
BINDING SITE FOR RESIDUE ZN B 390
2
AC2
SOFTWARE
ASP A:178 , HIS A:180 , ASP A:267 , 02G C:1
BINDING SITE FOR RESIDUE ZN A 390
3
AC3
SOFTWARE
ASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200
BINDING SITE FOR RESIDUE K B 391
4
AC4
SOFTWARE
ASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200
BINDING SITE FOR RESIDUE K A 391
5
AC5
SOFTWARE
PHE A:189 , THR A:192 , VAL A:195 , TYR A:225
BINDING SITE FOR RESIDUE K A 392
6
AC6
SOFTWARE
PHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , HOH B:429
BINDING SITE FOR RESIDUE K B 392
[
close Site info
]
SAPs(SNPs)/Variants
(4, 8)
Info
(mutated residues are only available for the asymmetric unit)
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)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
close PROSITE info
]
Exons
(0, 0)
Info
All Exons
View:
Select:
Label:
All Exon Boundaries
View:
Label:
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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
Chain C
Chain D
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 (132 KB)
Header - Asym.Unit
Biol.Unit 1 (64 KB)
Header - Biol.Unit 1
Biol.Unit 2 (65 KB)
Header - Biol.Unit 2
Biol.Unit 3 (125 KB)
Header - Biol.Unit 3
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
3RQD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
