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.
5THV
Asym. Unit
Info
Asym.Unit (131 KB)
Biol.Unit 1 (65 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 G305A HDAC8 IN COMPLEX WITH M344
Authors
:
N. J. Porter, D. W. Christianson
Date
:
30 Sep 16 (Deposition) - 21 Dec 16 (Release) - 21 Dec 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.87
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Zinc Histone Deactylase, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. J. Porter, N. H. Christianson, C. Decroos, D. W. Christianson
Structural And Functional Influence Of The Glycine-Rich Loo G302Gggy On The Catalytic Tyrosine Of Histone Deacetylase 8
Biochemistry V. 55 6718 2016
[
close entry info
]
Hetero Components
(4, 34)
Info
All Hetero Components
1a: 4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMI... (B3Na)
1b: 4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMI... (B3Nb)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
2e: 1,2-ETHANEDIOL (EDOe)
2f: 1,2-ETHANEDIOL (EDOf)
2g: 1,2-ETHANEDIOL (EDOg)
2h: 1,2-ETHANEDIOL (EDOh)
2i: 1,2-ETHANEDIOL (EDOi)
2j: 1,2-ETHANEDIOL (EDOj)
2k: 1,2-ETHANEDIOL (EDOk)
2l: 1,2-ETHANEDIOL (EDOl)
2m: 1,2-ETHANEDIOL (EDOm)
2n: 1,2-ETHANEDIOL (EDOn)
2o: 1,2-ETHANEDIOL (EDOo)
2p: 1,2-ETHANEDIOL (EDOp)
2q: 1,2-ETHANEDIOL (EDOq)
2r: 1,2-ETHANEDIOL (EDOr)
2s: 1,2-ETHANEDIOL (EDOs)
2t: 1,2-ETHANEDIOL (EDOt)
2u: 1,2-ETHANEDIOL (EDOu)
2v: 1,2-ETHANEDIOL (EDOv)
2w: 1,2-ETHANEDIOL (EDOw)
2x: 1,2-ETHANEDIOL (EDOx)
2y: 1,2-ETHANEDIOL (EDOy)
2z: 1,2-ETHANEDIOL (EDOz)
3a: POTASSIUM ION (Ka)
3b: POTASSIUM ION (Kb)
3c: POTASSIUM ION (Kc)
3d: POTASSIUM ION (Kd)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B3N
2
Ligand/Ion
4-(DIMETHYLAMINO)-N-[7-(HYDROXYAMINO)-7-OXOHEPTYL]BENZAMIDE
2
EDO
26
Ligand/Ion
1,2-ETHANEDIOL
3
K
4
Ligand/Ion
POTASSIUM ION
4
ZN
2
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(34, 34)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
24: AE6 (SOFTWARE)
25: AE7 (SOFTWARE)
26: AE8 (SOFTWARE)
27: AE9 (SOFTWARE)
28: AF1 (SOFTWARE)
29: AF2 (SOFTWARE)
30: AF3 (SOFTWARE)
31: AF4 (SOFTWARE)
32: AF5 (SOFTWARE)
33: AF6 (SOFTWARE)
34: AF7 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASP A:178 , HIS A:180 , ASP A:267 , B3N A:404
binding site for residue ZN A 401
02
AC2
SOFTWARE
ASP A:176 , ASP A:178 , HIS A:180 , SER A:199 , LEU A:200
binding site for residue K A 402
03
AC3
SOFTWARE
PHE A:189 , THR A:192 , VAL A:195 , TYR A:225 , HOH A:519 , HOH A:630
binding site for residue K A 403
04
AC4
SOFTWARE
HIS A:142 , HIS A:143 , PHE A:152 , ASP A:178 , HIS A:180 , ASP A:267 , GLY A:304 , TYR A:306 , ZN A:401 , EDO A:416 , HOH A:543 , ILE B:34 , PHE B:152 , PRO B:273 , TYR B:306 , B3N B:404
binding site for residue B3N A 404
05
AC5
SOFTWARE
PRO A:281 , VAL A:282 , TYR A:317 , LEU A:346 , GLU A:347 , ILE A:348 , HOH A:505 , HOH A:551
binding site for residue EDO A 405
06
AC6
SOFTWARE
ALA A:188 , HOH A:528
binding site for residue EDO A 406
07
AC7
SOFTWARE
VAL A:61 , SER A:63 , HIS A:360 , GLN A:363 , HOH A:641
binding site for residue EDO A 407
08
AC8
SOFTWARE
LYS A:132 , LEU A:292 , GLN A:295 , LEU A:296 , EDO A:412
binding site for residue EDO A 408
09
AC9
SOFTWARE
ALA A:68 , PHE A:70 , HIS A:71 , HOH A:504 , HOH A:516
binding site for residue EDO A 409
10
AD1
SOFTWARE
LYS A:374 , HIS A:375 , VAL A:376
binding site for residue EDO A 410
11
AD2
SOFTWARE
TYR A:317 , THR A:326 , LEU A:327 , SER A:329 , GLU A:347 , HOH A:551 , HOH A:568
binding site for residue EDO A 411
12
AD3
SOFTWARE
GLN A:293 , VAL A:321 , ILE A:322 , EDO A:408 , HOH A:512
binding site for residue EDO A 412
13
AD4
SOFTWARE
PHE A:208 , PRO A:209 , GLY A:210 , HOH A:518
binding site for residue EDO A 413
14
AD5
SOFTWARE
GLN A:236 , ASP A:237 , THR A:280 , PRO A:350 , HOH A:502 , HOH A:525 , HOH A:586
binding site for residue EDO A 414
15
AD6
SOFTWARE
TYR A:18 , ALA A:38 , VAL A:41 , HIS A:42 , SER A:138 , EDO A:418 , HOH A:511
binding site for residue EDO A 415
16
AD7
SOFTWARE
TRP A:141 , HIS A:142 , GLY A:151 , CYS A:153 , GLY A:304 , TYR A:306 , B3N A:404 , HOH A:642
binding site for residue EDO A 416
17
AD8
SOFTWARE
TRP A:141 , PHE A:152 , TYR A:154 , LEU A:155
binding site for residue EDO A 417
18
AD9
SOFTWARE
ARG A:37 , ALA A:38 , TRP A:137 , SER A:138 , TRP A:315 , EDO A:415 , HOH A:501
binding site for residue EDO A 418
19
AE1
SOFTWARE
ASP B:178 , HIS B:180 , ASP B:267 , B3N B:404
binding site for residue ZN B 401
20
AE2
SOFTWARE
ASP B:176 , ASP B:178 , HIS B:180 , SER B:199 , LEU B:200
binding site for residue K B 402
21
AE3
SOFTWARE
PHE B:189 , THR B:192 , VAL B:195 , TYR B:225 , HOH B:534 , HOH B:631
binding site for residue K B 403
22
AE4
SOFTWARE
LYS A:33 , ILE A:34 , PRO A:273 , TYR A:306 , B3N A:404 , HIS B:142 , HIS B:143 , PHE B:152 , ASP B:178 , HIS B:180 , ASP B:267 , GLY B:304 , TYR B:306 , ZN B:401 , HOH B:551 , HOH B:638
binding site for residue B3N B 404
23
AE5
SOFTWARE
ALA B:188 , HOH B:509 , HOH B:559
binding site for residue EDO B 405
24
AE6
SOFTWARE
PRO B:230 , ILE B:231 , GLN B:232 , ASN B:357 , ARG B:361 , ILE B:362 , ILE B:365 , EDO B:407 , HOH B:511
binding site for residue EDO B 406
25
AE7
SOFTWARE
PHE B:203 , ASP B:213 , ARG B:361 , EDO B:406
binding site for residue EDO B 407
26
AE8
SOFTWARE
PHE B:207 , PHE B:208 , PRO B:209 , GLY B:210 , EDO B:415 , HOH B:503 , HOH B:627
binding site for residue EDO B 408
27
AE9
SOFTWARE
PRO B:281 , VAL B:282 , TYR B:317 , LEU B:346 , GLU B:347 , ILE B:348 , HOH B:524 , HOH B:588
binding site for residue EDO B 409
28
AF1
SOFTWARE
CYS A:275 , ARG A:353 , LYS B:202 , SER B:204 , ASP B:233 , HOH B:518
binding site for residue EDO B 410
29
AF2
SOFTWARE
GLU B:65 , ALA B:68
binding site for residue EDO B 411
30
AF3
SOFTWARE
VAL B:214 , SER B:215 , TYR B:368 , ASN B:372
binding site for residue EDO B 412
31
AF4
SOFTWARE
TYR B:111 , TRP B:141 , PHE B:152 , CYS B:153 , TYR B:154 , LEU B:155
binding site for residue EDO B 413
32
AF5
SOFTWARE
VAL B:133 , LEU B:292 , GLN B:295 , LEU B:296
binding site for residue EDO B 414
33
AF6
SOFTWARE
SER B:150 , PHE B:208 , PRO B:209 , EDO B:408 , HOH B:510 , HOH B:578
binding site for residue EDO B 415
34
AF7
SOFTWARE
THR B:326
binding site for residue EDO B 416
[
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
(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
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 (131 KB)
Header - Asym.Unit
Biol.Unit 1 (65 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
5THV
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help