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.
PLEASE WAIT...
Getting 'Exon' information from database.
3WI6
Asym. Unit
Info
Asym.Unit (281 KB)
Biol.Unit 1 (543 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 MAPKAP KINASE-2 (MK2) IN COMPLEX WITH NON-SELECTIVE INHIBITOR
Authors
:
A. Fujino, K. Fukushima, T. Kubota, Y. Matsumoto, M. Takimoto-Kamimur
Date
:
06 Sep 13 (Deposition) - 18 Dec 13 (Release) - 18 Dec 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.99
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (2x)
Keywords
:
Gly-Rich Loop Formed, Atp-Binding, Kinase, Nucleotide-Binding, Phosphoprotein, Serine/Threonine-Protein Kinase, Transferase- Transferase Inhibitor Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Fujino, K. Fukushima, T. Kubota, Y. Matsumoto, M. Takimoto-Kamimura
Structure Of The Beta-Form Of Human Mk2 In Complex With The Non-Selective Kinase Inhibitor Tei-L03090
Acta Crystallogr. , Sect. F V. 69 1344 2013
[
close entry info
]
Hetero Components
(1, 6)
Info
All Hetero Components
1a: N-[(3S)-PIPERIDIN-3-YL]-7,8-DIHYDR... (YRZa)
1b: N-[(3S)-PIPERIDIN-3-YL]-7,8-DIHYDR... (YRZb)
1c: N-[(3S)-PIPERIDIN-3-YL]-7,8-DIHYDR... (YRZc)
1d: N-[(3S)-PIPERIDIN-3-YL]-7,8-DIHYDR... (YRZd)
1e: N-[(3S)-PIPERIDIN-3-YL]-7,8-DIHYDR... (YRZe)
1f: N-[(3S)-PIPERIDIN-3-YL]-7,8-DIHYDR... (YRZf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
YRZ
6
Ligand/Ion
N-[(3S)-PIPERIDIN-3-YL]-7,8-DIHYDRO-6H-PYRAZOLO[1,5-A]PYRROLO[3,2-E]PYRIMIDIN-5-AMINE
[
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
LEU A:70 , ALA A:91 , VAL A:118 , GLU A:139 , LEU A:141 , GLU A:190 , ASN A:191 , LEU A:193 , ASP A:207
BINDING SITE FOR RESIDUE YRZ A 901
2
AC2
SOFTWARE
LEU B:70 , VAL B:118 , GLU B:139 , LEU B:141 , GLU B:190 , ASN B:191 , LEU B:193 , ASP B:207
BINDING SITE FOR RESIDUE YRZ B 901
3
AC3
SOFTWARE
LEU C:70 , LEU C:72 , GLY C:73 , VAL C:118 , GLU C:139 , LEU C:141 , GLU C:190 , ASN C:191 , LEU C:193 , ASP C:207
BINDING SITE FOR RESIDUE YRZ C 901
4
AC4
SOFTWARE
LEU D:70 , VAL D:118 , GLU D:139 , LEU D:141 , GLU D:190 , ASN D:191 , LEU D:193 , ASP D:207
BINDING SITE FOR RESIDUE YRZ D 901
5
AC5
SOFTWARE
LEU E:70 , GLY E:73 , VAL E:118 , GLU E:139 , LEU E:141 , GLU E:190 , ASN E:191 , LEU E:193 , ASP E:207
BINDING SITE FOR RESIDUE YRZ E 901
6
AC6
SOFTWARE
LEU F:70 , GLY F:73 , VAL F:118 , GLU F:139 , LEU F:141 , GLU F:190 , ASN F:191 , LEU F:193 , ASP F:207
BINDING SITE FOR RESIDUE YRZ F 901
[
close Site info
]
SAPs(SNPs)/Variants
(1, 6)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_040753 (A173G, chain A/B/C/D/E/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_040753
A
173
G
MAPK2_HUMAN
Polymorphism
35671930
A/B/C/D/E/F
A
173
G
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 12)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (A:70-93,B:70-93,C:70-93,D:70-93,E:...)
2: PROTEIN_KINASE_ST (A:182-194,B:182-194,C:182-194,D:18...)
;
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.
MAPK2_HUMAN
70-93
6
A:70-93
B:70-93
C:70-93
D:70-93
E:70-93
F:70-93
2
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
MAPK2_HUMAN
182-194
6
A:182-194
B:182-194
C:182-194
D:182-194
E:182-194
F:182-194
[
close PROSITE info
]
Exons
(9, 54)
Info
All Exons
Exon 1.1b (A:46-93 | B:46-93 | C:46-93 | D:46...)
Exon 1.2 (A:94-140 | B:94-140 | C:94-140 | D...)
Exon 1.3b (A:140-162 (gaps) | B:140-162 (gaps...)
Exon 1.4b (A:162-188 | B:162-188 | C:162-188 ...)
Exon 1.5 (A:189-231 (gaps) | B:189-231 (gaps...)
Exon 1.6 (A:231-256 (gaps) | B:231-256 (gaps...)
Exon 1.7 (A:256-298 (gaps) | B:256-298 (gaps...)
Exon 1.8b (A:298-326 | B:298-326 | C:298-326 ...)
Exon 1.9b (A:327-347 | B:327-347 | C:327-347 ...)
View:
Select:
Label:
All Exon Boundaries
01: Boundary -/1.1b
02: Boundary 1.1b/1.2
03: Boundary 1.2/1.3b
04: Boundary 1.3b/1.4b
05: Boundary 1.4b/1.5
06: Boundary 1.5/1.6
07: Boundary 1.6/1.7
08: Boundary 1.7/1.8b
09: Boundary 1.8b/1.9b
10: Boundary 1.9b/1.9d
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1b
ENST00000367103
1b
ENSE00001825387
chr1:
206858382-206858853
472
MAPK2_HUMAN
1-93
93
6
A:46-93
B:46-93
C:46-93
D:46-93
E:46-93
F:46-93
48
48
48
48
48
48
1.2
ENST00000367103
2
ENSE00001069545
chr1:
206902055-206902194
140
MAPK2_HUMAN
94-140
47
6
A:94-140
B:94-140
C:94-140
D:94-140
E:94-140
F:94-140
47
47
47
47
47
47
1.3b
ENST00000367103
3b
ENSE00001069547
chr1:
206902380-206902444
65
MAPK2_HUMAN
140-162
23
6
A:140-162 (gaps)
B:140-162 (gaps)
C:140-162 (gaps)
D:140-162 (gaps)
E:140-162 (gaps)
F:140-162 (gaps)
23
23
23
23
23
23
1.4b
ENST00000367103
4b
ENSE00001069548
chr1:
206902741-206902820
80
MAPK2_HUMAN
162-188
27
6
A:162-188
B:162-188
C:162-188
D:162-188
E:162-188
F:162-188
27
27
27
27
27
27
1.5
ENST00000367103
5
ENSE00001069551
chr1:
206903317-206903443
127
MAPK2_HUMAN
189-231
43
6
A:189-231 (gaps)
B:189-231 (gaps)
C:189-231 (gaps)
D:189-231 (gaps)
E:189-231 (gaps)
F:189-231 (gaps)
43
43
43
43
43
43
1.6
ENST00000367103
6
ENSE00001648220
chr1:
206904033-206904108
76
MAPK2_HUMAN
231-256
26
6
A:231-256 (gaps)
B:231-256 (gaps)
C:231-256 (gaps)
D:231-256 (gaps)
E:231-256 (gaps)
F:231-256 (gaps)
26
26
26
26
26
26
1.7
ENST00000367103
7
ENSE00001069544
chr1:
206904483-206904607
125
MAPK2_HUMAN
256-298
43
6
A:256-298 (gaps)
B:256-298 (gaps)
C:256-298 (gaps)
D:256-298 (gaps)
E:256-298 (gaps)
F:256-298 (gaps)
43
43
43
43
43
43
1.8b
ENST00000367103
8b
ENSE00001069550
chr1:
206904985-206905070
86
MAPK2_HUMAN
298-326
29
6
A:298-326
B:298-326
C:298-326
D:298-326
E:298-326
F:298-326
29
29
29
29
29
29
1.9b
ENST00000367103
9b
ENSE00001069552
chr1:
206905184-206905264
81
MAPK2_HUMAN
327-353
27
6
A:327-347
B:327-347
C:327-347
D:327-347
E:327-347
F:327-347
21
21
21
21
21
21
1.9d
ENST00000367103
9d
ENSE00001443498
chr1:
206905920-206907628
1709
MAPK2_HUMAN
354-400
47
0
-
-
[
close EXON info
]
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d3wi6a_ (A:)
1b: SCOP_d3wi6b_ (B:)
1c: SCOP_d3wi6c_ (C:)
1d: SCOP_d3wi6d_ (D:)
1e: SCOP_d3wi6e_ (E:)
1f: SCOP_d3wi6f_ (F:)
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
:
MAP kinase activated protein kinase 2, mapkap2
(14)
Human (Homo sapiens) [TaxId: 9606]
(14)
1a
d3wi6a_
A:
1b
d3wi6b_
B:
1c
d3wi6c_
C:
1d
d3wi6d_
D:
1e
d3wi6e_
E:
1f
d3wi6f_
F:
[
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
Chain E
Chain F
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 (281 KB)
Header - Asym.Unit
Biol.Unit 1 (543 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
3WI6
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
