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.
1KGI
Asym. Unit
Info
Asym.Unit (90 KB)
Biol.Unit 1 (86 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
RAT TRANSTHYRETIN (ALSO CALLED PREALBUMIN) COMPLEX WITH 3, 3',5,5'-TETRAIODOTHYROACETIC ACID (T4AC)
Authors
:
A. Wojtczak, P. Neumann, T. Muziol, V. Cody, J. R. Luft, W. Pangborn
Date
:
27 Nov 01 (Deposition) - 27 Nov 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Prealbumin, Transport, Tetraiodothyroacetic Acid, Thyroid Ho, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Muziol, V. Cody, J. R. Luft, W. Pangborn, A. Wojtczak
Complex Of Rat Transthyretin With Tetraiodothyroacetic Acid Refined At 2. 1 And 1. 8 A Resolution.
Acta Biochim. Pol. V. 48 877 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 2)
Info
All Hetero Components
1a: 3,3',5,5'-TETRAIODOTHYROACETIC ACI... (T4Aa)
1b: 3,3',5,5'-TETRAIODOTHYROACETIC ACI... (T4Ab)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
T4A
2
Ligand/Ion
3,3',5,5'-TETRAIODOTHYROACETIC ACID
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS A:15 , LEU A:17 , THR A:106 , ALA A:108 , ALA A:109 , LEU A:110 , SER A:117 , THR A:119 , LYS C:415 , LEU C:417 , ALA C:508 , ALA C:509 , SER C:517 , THR C:518 , THR C:519 , HOH C:972 , HOH C:973 , SER D:715
BINDING SITE FOR RESIDUE T4A C 128
2
AC2
SOFTWARE
LYS B:215 , LEU B:217 , GLU B:254 , ALA B:308 , ALA B:309 , LEU B:310 , LYS D:615 , LEU D:617 , GLU D:654 , ALA D:708 , ALA D:709 , LEU D:710 , HOH D:995
BINDING SITE FOR RESIDUE T4A D 328
[
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, 8)
Info
All PROSITE Patterns/Profiles
1: TRANSTHYRETIN_1 (A:15-30,B:215-230,C:415-430,D:615-...)
2: TRANSTHYRETIN_2 (A:105-117,B:305-317,C:505-517,D:70...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TRANSTHYRETIN_1
PS00768
Transthyretin signature 1.
TTHY_RAT
35-50
4
A:15-30
B:215-230
C:415-430
D:615-630
2
TRANSTHYRETIN_2
PS00769
Transthyretin signature 2.
TTHY_RAT
125-137
4
A:105-117
B:305-317
C:505-517
D:705-717
[
close PROSITE info
]
Exons
(3, 12)
Info
All Exons
Exon 1.2 (A:8-47 | B:208-247 | C:407-447 | D...)
Exon 1.3 (A:47-92 | B:247-292 | C:447-492 | ...)
Exon 1.4 (A:93-127 | B:293-327 | C:493-527 |...)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.1/1.2
2: Boundary 1.2/1.3
3: Boundary 1.3/1.4
4: Boundary 1.4/-
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
1.1
ENSRNOT00000022113
1
ENSRNOE00000155027
chr18:
12406551-12406648
98
TTHY_RAT
1-23
23
0
-
-
1.2
ENSRNOT00000022113
2
ENSRNOE00000155619
chr18:
12407695-12407825
131
TTHY_RAT
24-67
44
4
A:8-47
B:208-247
C:407-447
D:608-647
40
40
41
40
1.3
ENSRNOT00000022113
3
ENSRNOE00000156091
chr18:
12410367-12410502
136
TTHY_RAT
67-112
46
4
A:47-92
B:247-292
C:447-492
D:647-692
46
46
46
46
1.4
ENSRNOT00000022113
4
ENSRNOE00000156567
chr18:
12413430-12413680
251
TTHY_RAT
113-147
35
4
A:93-127
B:293-327
C:493-527
D:693-727
35
35
35
35
[
close EXON info
]
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1kgia_ (A:)
1b: SCOP_d1kgib_ (B:)
1c: SCOP_d1kgic_ (C:)
1d: SCOP_d1kgid_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Prealbumin-like
(433)
Superfamily
:
Transthyretin (synonym: prealbumin)
(211)
Family
:
Transthyretin (synonym: prealbumin)
(198)
Protein domain
:
Transthyretin (synonym: prealbumin)
(194)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(4)
1a
d1kgia_
A:
1b
d1kgib_
B:
1c
d1kgic_
C:
1d
d1kgid_
D:
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_1kgiA00 (A:8-127)
1b: CATH_1kgiB00 (B:208-327)
1c: CATH_1kgiD00 (D:608-727)
1d: CATH_1kgiC00 (C:407-527)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.180, no name defined]
(150)
Norway rat (Rattus norvegicus)
(4)
1a
1kgiA00
A:8-127
1b
1kgiB00
B:208-327
1c
1kgiD00
D:608-727
1d
1kgiC00
C:407-527
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_Transthyretin_1kgiD01 (D:610-721)
1b: PFAM_Transthyretin_1kgiD02 (D:610-721)
1c: PFAM_Transthyretin_1kgiD03 (D:610-721)
1d: PFAM_Transthyretin_1kgiD04 (D:610-721)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Transthyretin
(88)
Family
:
Transthyretin
(45)
Rattus norvegicus (Rat)
(2)
1a
Transthyretin-1kgiD01
D:610-721
1b
Transthyretin-1kgiD02
D:610-721
1c
Transthyretin-1kgiD03
D:610-721
1d
Transthyretin-1kgiD04
D:610-721
[
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 (90 KB)
Header - Asym.Unit
Biol.Unit 1 (86 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
1KGI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
