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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
3ZNR
Asym. Unit
Info
Asym.Unit (173 KB)
Biol.Unit 1 (58 KB)
Biol.Unit 2 (61 KB)
Biol.Unit 3 (57 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HDAC7 BOUND WITH INHIBITOR TMP269
Authors
:
M. Lobera, K. Madauss, D. Pohlhaus, R. Trump, M. Nolan
Date
:
15 Feb 13 (Deposition) - 27 Mar 13 (Release) - 01 May 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Keywords
:
Hydrolase, Class Iia Hdacs, Tfmo
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Lobera, K. P. Madauss, D. T. Pohlhaus, Q. G. Wright, M. Trocha, D. R. Schmidt, E. Baloglu, R. P. Trump, M. S. Head, G. A. Hofmann, M. Murray-Thompson, B. Schwartz, S. Chakravorty, Z. Wu, P. K. Mander, L. Kruidenier, R. A. Reid, W. Burkhart, B. J. Turunen, J. X. Rong, C. Wagner, M. B. Moyer, C. Wells, X. Hong, J. T. Moore, J. D. Williams, D. Soler, S. Ghosh, M. A. Nolan
Selective Class Iia Histone Deacetylase Inhibition Via A Non-Chelating Zinc Binding Group
Nat. Chem. Biol. V. 9 319 2013
[
close entry info
]
Hetero Components
(3, 13)
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: N-{[4-(4-PHENYL-1,3-THIAZOL-2-YL)T... (NU9a)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
K
6
Ligand/Ion
POTASSIUM ION
2
NU9
1
Ligand/Ion
N-{[4-(4-PHENYL-1,3-THIAZOL-2-YL)TETRAHYDRO-2H-PYRAN-4-YL]METHYL}-3-[5-(TRIFLUOROMETHYL)-1,2,4-OXADIAZOL-3-YL]BENZAMIDE
3
ZN
6
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:707 , HIS A:709 , ASP A:801 , NU9 A:1000
BINDING SITE FOR RESIDUE ZN A 101
02
AC2
SOFTWARE
CYS A:533 , CYS A:535 , HIS A:541 , CYS A:618
BINDING SITE FOR RESIDUE ZN A 102
03
AC3
SOFTWARE
ASP A:705 , ASP A:707 , HIS A:709 , SER A:728 , LEU A:729
BINDING SITE FOR RESIDUE K A 201
04
AC4
SOFTWARE
PHE A:718 , ASP A:721 , VAL A:724 , PHE A:755 , HOH A:2014 , HOH A:2015
BINDING SITE FOR RESIDUE K A 202
05
AC5
SOFTWARE
ASP B:707 , HIS B:709 , ASP B:801
BINDING SITE FOR RESIDUE ZN B 101
06
AC6
SOFTWARE
CYS B:533 , CYS B:535 , HIS B:541 , CYS B:618
BINDING SITE FOR RESIDUE ZN B 102
07
AC7
SOFTWARE
ASP B:705 , ASP B:707 , HIS B:709 , SER B:728 , LEU B:729
BINDING SITE FOR RESIDUE K B 201
08
AC8
SOFTWARE
PHE B:718 , ASP B:721 , VAL B:724 , PHE B:755 , HOH B:2017 , HOH B:2018
BINDING SITE FOR RESIDUE K B 202
09
AC9
SOFTWARE
ASP C:707 , HIS C:709 , ASP C:801
BINDING SITE FOR RESIDUE ZN C 101
10
BC1
SOFTWARE
CYS C:533 , CYS C:535 , HIS C:541 , CYS C:618
BINDING SITE FOR RESIDUE ZN C 102
11
BC2
SOFTWARE
ASP C:705 , ASP C:707 , HIS C:709 , SER C:728 , LEU C:729
BINDING SITE FOR RESIDUE K C 201
12
BC3
SOFTWARE
PHE C:718 , VAL C:724 , PHE C:755 , HOH C:2003 , HOH C:2004
BINDING SITE FOR RESIDUE K C 202
13
BC4
SOFTWARE
ZN A:101 , PRO A:542 , GLU A:543 , PRO A:667 , HIS A:669 , HIS A:670 , GLY A:678 , PHE A:679 , CYS A:680 , ASP A:707 , HIS A:709 , PHE A:738 , ASP A:801 , PRO A:809 , LEU A:810 , GLU A:840 , GLY A:841 , HIS A:843
BINDING SITE FOR RESIDUE NU9 A1000
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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
(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.
SCOP Domains
(1, 3)
Info
All SCOP Domains
1a: SCOP_d3znra_ (A:)
1b: SCOP_d3znrb_ (B:)
1c: SCOP_d3znrc_ (C:)
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
:
Histone deacetylase 7, HDAC7
(5)
Human (Homo sapiens) [TaxId: 9606]
(5)
1a
d3znra_
A:
1b
d3znrb_
B:
1c
d3znrc_
C:
[
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
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 (173 KB)
Header - Asym.Unit
Biol.Unit 1 (58 KB)
Header - Biol.Unit 1
Biol.Unit 2 (61 KB)
Header - Biol.Unit 2
Biol.Unit 3 (57 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
3ZNR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help