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.
2F2C
Biol. Unit 1
Info
Asym.Unit (89 KB)
Biol.Unit 1 (82 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY STRUCTURE OF HUMAN CDK6-VCYCLINWITH THE INHIBITOR AMINOPURVALANOL
Authors
:
U Schulze-Gahmen, H. Lu
Date
:
16 Nov 05 (Deposition) - 13 Jun 06 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Small Molecule Inhibitor Bound Between N-Terminal And C-Terminal Domain Of Kinase, Cell Cycle-Transferase Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
H. Lu, U. Schulze-Gahmen
Toward Understanding The Structural Basis Of Cyclin-Dependent Kinase 6 Specific Inhibition.
J. Med. Chem. V. 49 3826 2006
[
close entry info
]
Hetero Components
(3, 3)
Info
All Hetero Components
1a: (2S)-2-({6-[(3-AMINO-5-CHLOROPHENY... (AP9a)
2a: DIMETHYL SULFOXIDE (DMSa)
3a: SULFATE ION (SO4a)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
AP9
1
Ligand/Ion
(2S)-2-({6-[(3-AMINO-5-CHLOROPHENYL)AMINO]-9-ISOPROPYL-9H-PURIN-2-YL}AMINO)-3-METHYLBUTAN-1-OL
2
DMS
1
Ligand/Ion
DIMETHYL SULFOXIDE
3
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
VAL A:111 , ARG B:60 , ARG B:144 , ARG B:168 , MET B:174 , ALA B:175 , LEU B:176 , THR B:177 , TYR B:196
BINDING SITE FOR RESIDUE SO4 B 402
2
AC2
SOFTWARE
ILE B:19 , GLY B:20 , VAL B:27 , ALA B:41 , VAL B:77 , PHE B:98 , GLU B:99 , VAL B:101 , ASP B:102 , GLN B:103 , ASP B:104 , THR B:107 , GLN B:149 , LEU B:152
BINDING SITE FOR RESIDUE AP9 B 401
3
AC3
SOFTWARE
LEU B:65 , LEU B:68 , GLU B:69 , HIS B:73 , VAL B:77
BINDING SITE FOR RESIDUE DMS B 403
[
close Site info
]
SAPs(SNPs)/Variants
(3, 3)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_041978 (D110N, chain B, )
2: VAR_072638 (A197T, chain B, )
3: VAR_041979 (P199L, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_041978
D
110
N
CDK6_HUMAN
Polymorphism
35654944
B
D
110
N
2
UniProt
VAR_072638
A
197
T
CDK6_HUMAN
Disease (MCPH12)
---
B
A
197
T
3
UniProt
VAR_041979
P
199
L
CDK6_HUMAN
Unclassified
---
B
P
199
L
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(3, 3)
Info
All PROSITE Patterns/Profiles
1: PROTEIN_KINASE_ATP (B:19-43)
2: CYCLINS (A:52-83)
3: PROTEIN_KINASE_ST (B:141-153)
;
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.
CDK6_HUMAN
19-43
1
B:19-43
2
CYCLINS
PS00292
Cyclins signature.
CGH2_SHV21
52-83
1
A:52-83
3
PROTEIN_KINASE_ST
PS00108
Serine/Threonine protein kinases active-site signature.
CDK6_HUMAN
141-153
1
B:141-153
[
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
(2, 3)
Info
All SCOP Domains
1a: SCOP_d2f2ca1 (A:8-148)
1b: SCOP_d2f2ca2 (A:149-254)
2a: SCOP_d2f2cb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Cyclin-like
(137)
Superfamily
:
Cyclin-like
(137)
Family
:
Cyclin
(117)
Protein domain
:
Viral cyclin
(7)
Herpesvirus saimiri [TaxId: 10381]
(5)
1a
d2f2ca1
A:8-148
1b
d2f2ca2
A:149-254
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
:
Cyclin-dependent PK, CDK6
(11)
Human (Homo sapiens) [TaxId: 9606]
(11)
2a
d2f2cb_
B:
[
close SCOP info
]
CATH Domains
(3, 4)
Info
all CATH domains
1a: CATH_2f2cB01 (B:11-102)
2a: CATH_2f2cA01 (A:37-148)
2b: CATH_2f2cA02 (A:149-254)
3a: CATH_2f2cB02 (B:103-299)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Phosphorylase Kinase; domain 1
(1392)
Homologous Superfamily
:
Phosphorylase Kinase; domain 1
(1392)
Herpesvirus saimiri (strain 11). Organism_taxid: 10383. Strain: 11.
(2)
1a
2f2cB01
B:11-102
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Cyclin A; domain 1
(136)
Homologous Superfamily
:
[code=1.10.472.10, no name defined]
(99)
Herpesvirus saimiri (strain 11). Organism_taxid: 10383. Strain: 11.
(3)
2a
2f2cA01
A:37-148
2b
2f2cA02
A:149-254
Topology
:
Transferase(Phosphotransferase); domain 1
(1379)
Homologous Superfamily
:
Transferase(Phosphotransferase) domain 1
(1379)
Herpesvirus saimiri (strain 11). Organism_taxid: 10383. Strain: 11.
(2)
3a
2f2cB02
B:103-299
[
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 (89 KB)
Header - Asym.Unit
Biol.Unit 1 (82 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
2F2C
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
