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.
4DGM
Asym. Unit
Info
Asym.Unit (125 KB)
Biol.Unit 1 (120 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 MAIZE CK2 IN COMPLEX WITH THE INHIBITOR APIGENIN
Authors
:
G. Lolli, M. Mazzorana, R. Battistutta
Date
:
26 Jan 12 (Deposition) - 01 Aug 12 (Release) - 02 Jan 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.65
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Protein Kinase, Transferase-Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
G. Lolli, G. Cozza, M. Mazzorana, E. Tibaldi, L. Cesaro, A. Donella-Deana, F. Meggio, A. Venerando, C. Franchin, S. Sarno, R. Battistutta, L. A. Pinna
Inhibition Of Protein Kinase Ck2 By Flavonoids And Tyrphostins. A Structural Insight.
Biochemistry V. 51 6097 2012
[
close entry info
]
Hetero Components
(3, 6)
Info
All Hetero Components
1a: 5,7-DIHYDROXY-2-(4-HYDROXYPHENYL)-... (AGIa)
2a: 1,2-ETHANEDIOL (EDOa)
2b: 1,2-ETHANEDIOL (EDOb)
2c: 1,2-ETHANEDIOL (EDOc)
2d: 1,2-ETHANEDIOL (EDOd)
3a: DI(HYDROXYETHYL)ETHER (PEGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AGI
1
Ligand/Ion
5,7-DIHYDROXY-2-(4-HYDROXYPHENYL)-4H-CHROMEN-4-ONE
2
EDO
4
Ligand/Ion
1,2-ETHANEDIOL
3
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
[
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
TYR A:125 , MET A:221 , GLY A:224 , MET A:225 , GLU A:230 , HOH A:659
BINDING SITE FOR RESIDUE EDO A 401
2
AC2
SOFTWARE
THR A:129 , ASP A:130 , HIS A:291 , HOH A:553
BINDING SITE FOR RESIDUE EDO A 402
3
AC3
SOFTWARE
VAL A:11 , SER A:212 , MET A:215 , ARG A:312 , LEU A:313 , THR A:314 , HOH A:516 , HOH A:634 , HOH A:635
BINDING SITE FOR RESIDUE EDO A 403
4
AC4
SOFTWARE
ALA A:9 , TYR A:12 , ALA A:13 , ASP A:14 , GLN A:325
BINDING SITE FOR RESIDUE EDO A 404
5
AC5
SOFTWARE
ARG A:278 , ASP A:302 , LEU A:305 , ARG A:306 , TYR A:307 , ASP A:308 , GLU A:311 , HOH A:592
BINDING SITE FOR RESIDUE PEG A 405
6
AC6
SOFTWARE
VAL A:45 , VAL A:53 , ILE A:66 , LYS A:68 , PHE A:113 , VAL A:116 , ASN A:118 , MET A:163 , ILE A:174 , ASP A:175 , HOH A:501 , HOH A:581
BINDING SITE FOR RESIDUE AGI A 406
[
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
(2, 2)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:45-68)
2: PROTEIN_KINASE_ST (A:152-164)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PROTEIN_KINASE_ATP
PS00107
Protein kinases ATP-binding region signature.
CSK2A_MAIZE
40-63
1
A:45-68
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
CSK2A_MAIZE
147-159
1
A:152-164
[
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, 1)
Info
All SCOP Domains
1a: SCOP_d4dgma_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Protein kinase-like (PK-like)
(2589)
Superfamily
:
Protein kinase-like (PK-like)
(2589)
Family
:
Protein kinases, catalytic subunit
(1977)
Protein domain
:
Protein kinase CK2, alpha subunit
(68)
Maize (Zea mays) [TaxId: 4577]
(31)
1a
d4dgma_
A:
[
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 (125 KB)
Header - Asym.Unit
Biol.Unit 1 (120 KB)
Header - Biol.Unit 1
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
4DGM
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help