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.
5J3Z
Biol. Unit 1
Info
Asym.Unit (188 KB)
Biol.Unit 1 (94 KB)
Biol.Unit 2 (91 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 M2HTDP2-CAT IN COMPLEX WITH A SMALL MOLECULE INHIBITOR
Authors
:
P. Hornyak, L. H. Pearl, K. W. Caldecott, A. W. Oliver
Date
:
31 Mar 16 (Deposition) - 04 May 16 (Release) - 06 Jul 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Tyrosyl Dna Phosphodiesterase 2 Catalytic Domain, Hydrolase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Hornyak, T. Askwith, S. Walker, E. Komulainen, M. Paradowski, L. E. Pennicott, E. J. Bartlett, N. C. Brissett, A. Raoof, M. Watson, A. M. Jordan, D. J. Ogilvie, S. E. Ward, J. R. Atack, L. H. Pearl, K. W. Caldecott, A. W. Oliver
Mode Of Action Of Dna-Competitive Small Molecule Inhibitors Of Tyrosyl Dna Phosphodiesterase 2.
Biochem. J. V. 473 1869 2016
[
close entry info
]
Hetero Components
(4, 15)
Info
All Hetero Components
1a: 2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)... (6FQa)
1b: 2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)... (6FQb)
2a: ACETATE ION (ACTa)
2b: ACETATE ION (ACTb)
2c: ACETATE ION (ACTc)
2d: ACETATE ION (ACTd)
2e: ACETATE ION (ACTe)
2f: ACETATE ION (ACTf)
3a: 1,2-ETHANEDIOL (EDOa)
3b: 1,2-ETHANEDIOL (EDOb)
3c: 1,2-ETHANEDIOL (EDOc)
3d: 1,2-ETHANEDIOL (EDOd)
3e: 1,2-ETHANEDIOL (EDOe)
3f: 1,2-ETHANEDIOL (EDOf)
3g: 1,2-ETHANEDIOL (EDOg)
3h: 1,2-ETHANEDIOL (EDOh)
3i: 1,2-ETHANEDIOL (EDOi)
3j: 1,2-ETHANEDIOL (EDOj)
3k: 1,2-ETHANEDIOL (EDOk)
3l: 1,2-ETHANEDIOL (EDOl)
3m: 1,2-ETHANEDIOL (EDOm)
3n: 1,2-ETHANEDIOL (EDOn)
3o: 1,2-ETHANEDIOL (EDOo)
4a: GLYCEROL (GOLa)
4b: GLYCEROL (GOLb)
4c: GLYCEROL (GOLc)
4d: GLYCEROL (GOLd)
5a: MAGNESIUM ION (MGa)
5b: MAGNESIUM ION (MGb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
6FQ
1
Ligand/Ion
2,4-DIOXO-10-[3-(1H-TETRAZOL-5-YL)PHENYL]-2,3,4,10-TETRAHYDROPYRIMIDO[4,5-B]QUINOLINE-8-CARBONITRILE
2
ACT
1
Ligand/Ion
ACETATE ION
3
EDO
11
Ligand/Ion
1,2-ETHANEDIOL
4
GOL
2
Ligand/Ion
GLYCEROL
5
MG
-1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(17, 17)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:240 , ARG A:241 , ARG A:276 , ILE A:317 , CYS A:321 , LEU A:323 , HOH A:534 , HOH A:625 , HOH A:648 , ILE B:317 , PRO B:318 , 6FQ B:401
binding site for residue 6FQ A 401
02
AC2
SOFTWARE
ASP A:132 , GLU A:162 , HOH A:501 , HOH A:502 , HOH A:510 , HOH A:535 , HOH A:715 , ARG B:316
binding site for residue MG A 402
03
AC3
SOFTWARE
TRP A:307 , ASP A:358 , HIS A:359 , EDO A:409 , HOH A:502 , HOH A:535 , HOH A:563 , HOH A:679 , PRO B:318 , HOH B:572
binding site for residue GOL A 403
04
AC4
SOFTWARE
GLY A:256 , GLN A:259 , PRO A:287 , HOH A:657
binding site for residue GOL A 404
05
AC5
SOFTWARE
VAL A:199 , LYS A:200 , PHE A:201 , HOH A:569 , HOH A:583
binding site for residue EDO A 405
06
AC6
SOFTWARE
LYS A:301 , HIS A:302 , GLN A:304 , TYR A:305 , ASP A:308 , LEU A:344 , TRP A:360 , HOH A:550
binding site for residue EDO A 406
07
AC7
SOFTWARE
ASN A:184 , GLU A:186 , TYR A:188 , PHE A:189 , MET A:214 , MET A:215 , HOH A:522 , HOH A:605 , HOH A:699
binding site for residue EDO A 407
08
AC8
SOFTWARE
ASP A:156 , ARG A:198 , EDO A:410 , EDO A:411 , HOH A:514 , HOH A:562
binding site for residue EDO A 408
09
AC9
SOFTWARE
ASN A:130 , GLU A:162 , HIS A:236 , SER A:239 , ASP A:272 , ASN A:274 , HIS A:359 , GOL A:403 , HOH A:579
binding site for residue EDO A 409
10
AD1
SOFTWARE
THR A:123 , ASP A:156 , GLY A:226 , EDO A:408 , HOH A:612
binding site for residue EDO A 410
11
AD2
SOFTWARE
EDO A:408 , HOH A:606 , HOH A:669
binding site for residue EDO A 411
12
AD3
SOFTWARE
HOH A:515 , HOH A:539 , HOH A:551
binding site for residue EDO A 412
13
AD4
SOFTWARE
ARG A:241 , SER A:244 , ASP A:277 , GLU A:279
binding site for residue EDO A 413
14
AD5
SOFTWARE
HIS A:302 , SER A:341 , LEU A:342 , ASP A:343 , HOH A:548 , HOH A:559
binding site for residue EDO A 414
15
AD6
SOFTWARE
ASN A:289 , PHE A:291 , ALA A:332 , GLU A:334
binding site for residue EDO A 415
16
AD7
SOFTWARE
LEU A:152 , HOH A:529
binding site for residue ACT A 416
17
AD8
SOFTWARE
ILE A:317 , PRO A:318 , ALA A:319 , 6FQ A:401 , THR B:240 , ARG B:241 , ARG B:276 , ARG B:278 , ILE B:317 , CYS B:321 , LEU B:323 , HOH B:610 , HOH B:624
binding site for residue 6FQ B 401
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
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
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 (188 KB)
Header - Asym.Unit
Biol.Unit 1 (94 KB)
Header - Biol.Unit 1
Biol.Unit 2 (91 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
5J3Z
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help