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.
1IC2
Asym. Unit
Info
Asym.Unit (59 KB)
Biol.Unit 1 (29 KB)
Biol.Unit 2 (28 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
DECIPHERING THE DESIGN OF THE TROPOMYOSIN MOLECULE
Authors
:
J. H. Brown, K. -H. Kim, G. Jun, N. J. Greenfield, R. Dominguez, N. Volkmann, S. E. Hitchcock-Degregori, C. Cohen
Date
:
29 Mar 01 (Deposition) - 25 Jul 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Alpha-Helical Coiled Coil, Alanine, Symmetry, Axial Stagger, Bend, Contractile Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. H. Brown, K. -H. Kim, G. Jun, N. J. Greenfield, R. Dominguez, N. Volkmann, S. E. Hitchcock-Degregori, C. Cohen
Deciphering The Design Of The Tropomyosin Molecule
Proc. Natl. Acad. Sci. Usa V. 98 8496 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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
(2, 8)
Info
All Exons
Exon 1.1d (A:1-38 | B:1-38 | C:1-38 | D:1-38)
Exon 1.3 (A:39-79 | B:39-77 | C:39-79 | D:39...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary -/1.1d
2: Boundary 1.1d/1.3
3: Boundary 1.3/1.6
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
1.1d
ENSGALT00000005572
1d
ENSGALE00000035748
chr10:
5126807-5126694
114
TPM1_CHICK
1-38
38
4
A:1-38
B:1-38
C:1-38
D:1-38
38
38
38
38
1.3
ENSGALT00000005572
3
ENSGALE00000035746
chr10:
5125697-5125572
126
TPM1_CHICK
39-80
42
4
A:39-79
B:39-77
C:39-79
D:39-77
41
39
41
39
1.6
ENSGALT00000005572
6
ENSGALE00000261249
chr10:
5119184-5119051
134
TPM1_CHICK
81-125
45
0
-
-
1.7
ENSGALT00000005572
7
ENSGALE00000035741
chr10:
5117763-5117646
118
TPM1_CHICK
125-164
40
0
-
-
1.8
ENSGALT00000005572
8
ENSGALE00000035743
chr10:
5117525-5117455
71
TPM1_CHICK
165-188
24
0
-
-
1.10
ENSGALT00000005572
10
ENSGALE00000035749
chr10:
5116647-5116572
76
TPM1_CHICK
188-213
26
0
-
-
1.11
ENSGALT00000005572
11
ENSGALE00000035745
chr10:
5116155-5116093
63
TPM1_CHICK
214-234
21
0
-
-
1.12
ENSGALT00000005572
12
ENSGALE00000261199
chr10:
5115818-5115749
70
TPM1_CHICK
235-258
24
0
-
-
1.13b
ENSGALT00000005572
13b
ENSGALE00000145267
chr10:
5114603-5114519
85
TPM1_CHICK
258-284
27
0
-
-
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1ic2a_ (A:)
1b: SCOP_d1ic2b_ (B:)
1c: SCOP_d1ic2c_ (C:)
1d: SCOP_d1ic2d_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Coiled coil proteins
(689)
Fold
:
Parallel coiled-coil
(407)
Superfamily
:
Tropomyosin
(10)
Family
:
Tropomyosin
(9)
Protein domain
:
Tropomyosin
(9)
Chicken (Gallus gallus) [TaxId: 9031]
(1)
1a
d1ic2a_
A:
1b
d1ic2b_
B:
1c
d1ic2c_
C:
1d
d1ic2d_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1ic2B00 (B:1-77)
1b: CATH_1ic2D00 (D:1-77)
1c: CATH_1ic2A00 (A:1-79)
1d: CATH_1ic2C00 (C:1-79)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Up-down Bundle
(3216)
Topology
:
Single alpha-helices involved in coiled-coils or other helix-helix interfaces
(552)
Homologous Superfamily
:
[code=1.20.5.340, no name defined]
(4)
Chicken (Gallus gallus)
(1)
1a
1ic2B00
B:1-77
1b
1ic2D00
D:1-77
1c
1ic2A00
A:1-79
1d
1ic2C00
C:1-79
[
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
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 (59 KB)
Header - Asym.Unit
Biol.Unit 1 (29 KB)
Header - Biol.Unit 1
Biol.Unit 2 (28 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
1IC2
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help