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.
3IMY
Asym. Unit
Info
Asym.Unit (48 KB)
Biol.Unit 1 (44 KB)
Biol.Unit 2 (85 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF TR-BETA BOUND TO SELECTIVE THYROMIMETIC GC-1
Authors
:
L. Bleicher, L. Polikarpov, R. Aparicio
Date
:
11 Aug 09 (Deposition) - 08 Sep 09 (Release) - 08 Sep 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.55
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Biol. Unit 2: A (2x)
Keywords
:
Alternative Splicing, Deafness, Disease Mutation, Dna- Binding, Metal-Binding, Nucleus, Polymorphism, Receptor, Transcription, Transcription Regulation, Zinc, Zinc-Finger, Nuclear Protein Receptor
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Bleicher, R. Aparicio, F. M. Nunes, L. Martinez, S. M. Gomes Dias, A. C. M. Figueira, M. A. M. Santos, W. H. Venturelli, R. Da Silva, P. M. Donate, F. A. Neves, L. A. Simeoni, J. D. Baxter, P. Webb, M. S. Skaf, I. Polikarpov
Structural Basis Of Gc-1 Selectivity For Thyroid Hormone Receptor Isoforms.
Bmc Struct. Biol. V. 8 1 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(2, 4)
Info
All Hetero Components
1a: {4-[4-HYDROXY-3-(1-METHYLETHYL)BEN... (B72a)
2a: S-(DIMETHYLARSENIC)CYSTEINE (CASa)
2b: S-(DIMETHYLARSENIC)CYSTEINE (CASb)
2c: S-(DIMETHYLARSENIC)CYSTEINE (CASc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
B72
1
Ligand/Ion
{4-[4-HYDROXY-3-(1-METHYLETHYL)BENZYL]-3,5-DIMETHYLPHENOXY}ACETIC ACID
2
CAS
3
Mod. Amino Acid
S-(DIMETHYLARSENIC)CYSTEINE
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
HOH A:1 , HOH A:55 , ALA A:279 , ARG A:282 , MET A:313 , LEU A:330 , ASN A:331 , GLY A:344 , LEU A:346 , HIS A:435 , PHE A:455
BINDING SITE FOR RESIDUE B72 A 462
[
close Site info
]
SAPs(SNPs)/Variants
(35, 35)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_050577 (D216G, chain A, )
02: VAR_004632 (A234T, chain A, )
03: VAR_004633 (R243W, chain A, )
04: VAR_059041 (A268G, chain A, )
05: VAR_004634 (R316H, chain A, )
06: VAR_004635 (A317T, chain A, )
07: VAR_004636 (R320C, chain A, )
08: VAR_004637 (R320H, chain A, )
09: VAR_059042 (N331D, chain A, )
10: VAR_004638 (G332R, chain A, )
11: VAR_059043 (A335P, chain A, )
12: VAR_011784 (T337I, chain A, )
13: VAR_004640 (R338W, chain A, )
14: VAR_004641 (Q340H, chain A, )
15: VAR_059044 (L341P, chain A, )
16: VAR_004642 (K342I, chain A, )
17: VAR_004645 (G345R, chain A, )
18: VAR_004644 (G345S, chain A, )
19: VAR_004643 (G345V, chain A, )
20: VAR_059045 (L346F, chain A, )
21: VAR_004646 (G347E, chain A, )
22: VAR_004647 (V348E, chain A, )
23: VAR_004648 (T426I, chain A, )
24: VAR_058508 (R429Q, chain A, )
25: VAR_059046 (I431M, chain A, )
26: VAR_004649 (R438H, chain A, )
27: VAR_004650 (M442V, chain A, )
28: VAR_004651 (K443E, chain A, )
29: VAR_004652 (C446R, chain A, )
30: VAR_059047 (P447T, chain A, )
31: VAR_004653 (P453H, chain A, )
32: VAR_059048 (P453L, chain A, )
33: VAR_004654 (P453S, chain A, )
34: VAR_004655 (P453T, chain A, )
35: VAR_059049 (F459C, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_050577
D
216
G
THB_HUMAN
Polymorphism
9865746
A
D
216
G
02
UniProt
VAR_004632
A
234
T
THB_HUMAN
Disease (GTHR)
---
A
A
234
T
03
UniProt
VAR_004633
R
243
W
THB_HUMAN
Disease (GTHR)
---
A
R
243
W
04
UniProt
VAR_059041
A
268
G
THB_HUMAN
Disease (GTHR)
---
A
A
268
G
05
UniProt
VAR_004634
R
316
H
THB_HUMAN
Disease (PRTH)
---
A
R
316
H
06
UniProt
VAR_004635
A
317
T
THB_HUMAN
Disease (GTHR)
---
A
A
317
T
07
UniProt
VAR_004636
R
320
C
THB_HUMAN
Disease (GTHR)
---
A
R
320
C
08
UniProt
VAR_004637
R
320
H
THB_HUMAN
Disease (GTHR)
---
A
R
320
H
09
UniProt
VAR_059042
N
331
D
THB_HUMAN
Disease (GTHR)
---
A
N
331
D
10
UniProt
VAR_004638
G
332
R
THB_HUMAN
Disease (GTHR)
28999969
A
G
332
R
11
UniProt
VAR_059043
A
335
P
THB_HUMAN
Disease (GTHR)
---
A
A
335
P
12
UniProt
VAR_011784
T
337
I
THB_HUMAN
Polymorphism
1054624
A
T
337
I
13
UniProt
VAR_004640
R
338
W
THB_HUMAN
Disease (GTHR)
---
A
R
338
W
14
UniProt
VAR_004641
Q
340
H
THB_HUMAN
Disease (GTHR)
---
A
Q
340
H
15
UniProt
VAR_059044
L
341
P
THB_HUMAN
Disease (GTHR)
---
A
L
341
P
16
UniProt
VAR_004642
K
342
I
THB_HUMAN
Disease (GTHR)
---
A
K
342
I
17
UniProt
VAR_004645
G
345
R
THB_HUMAN
Disease (GTHR)
---
A
G
345
R
18
UniProt
VAR_004644
G
345
S
THB_HUMAN
Disease (GTHR)
---
A
G
345
S
19
UniProt
VAR_004643
G
345
V
THB_HUMAN
Disease (GTHR)
28999970
A
G
345
V
20
UniProt
VAR_059045
L
346
F
THB_HUMAN
Disease (GTHR)
---
A
L
346
F
21
UniProt
VAR_004646
G
347
E
THB_HUMAN
Disease (GTHR)
28999971
A
G
347
E
22
UniProt
VAR_004647
V
348
E
THB_HUMAN
Disease (GTHR)
---
A
V
348
E
23
UniProt
VAR_004648
T
426
I
THB_HUMAN
Disease (GTHR)
---
A
T
426
I
24
UniProt
VAR_058508
R
429
Q
THB_HUMAN
Disease (PRTH)
---
A
R
429
Q
25
UniProt
VAR_059046
I
431
M
THB_HUMAN
Disease (GTHR)
---
A
I
431
M
26
UniProt
VAR_004649
R
438
H
THB_HUMAN
Disease (GTHR)
---
A
R
438
H
27
UniProt
VAR_004650
M
442
V
THB_HUMAN
Disease (GTHR)
---
A
M
442
V
28
UniProt
VAR_004651
K
443
E
THB_HUMAN
Disease (GTHR)
---
A
K
443
E
29
UniProt
VAR_004652
C
446
R
THB_HUMAN
Disease (GTHR)
---
A
C
446
R
30
UniProt
VAR_059047
P
447
T
THB_HUMAN
Disease (GTHR)
---
A
P
447
T
31
UniProt
VAR_004653
P
453
H
THB_HUMAN
Disease (GTHR)
---
A
P
453
H
32
UniProt
VAR_059048
P
453
L
THB_HUMAN
Disease (GTHR)
---
A
P
453
L
33
UniProt
VAR_004654
P
453
S
THB_HUMAN
Disease (GTHR)
---
A
P
453
S
34
UniProt
VAR_004655
P
453
T
THB_HUMAN
Disease (GTHR)
28933408
A
P
453
T
35
UniProt
VAR_059049
F
459
C
THB_HUMAN
Disease (GTHR)
---
A
F
459
C
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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
(4, 4)
Info
All Exons
Exon 1.14 (A:201-246)
Exon 1.15 (A:247-295 (gaps))
Exon 1.16 (A:296-382)
Exon 1.17d (A:382-461)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.13b/1.14
2: Boundary 1.14/1.15
3: Boundary 1.15/1.16
4: Boundary 1.16/1.17d
5: Boundary 1.17d/-
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
1.2g
ENST00000396671
2g
ENSE00001687497
chr3:
24536266-24536178
89
THB_HUMAN
-
0
0
-
-
1.5
ENST00000396671
5
ENSE00001395906
chr3:
24378862-24378791
72
THB_HUMAN
-
0
0
-
-
1.7a
ENST00000396671
7a
ENSE00001612462
chr3:
24338862-24338717
146
THB_HUMAN
-
0
0
-
-
1.8b
ENST00000396671
8b
ENSE00001397913
chr3:
24270492-24270429
64
THB_HUMAN
1-8
8
0
-
-
1.10c
ENST00000396671
10c
ENSE00001693312
chr3:
24231825-24231565
261
THB_HUMAN
8-95
88
0
-
-
1.12e
ENST00000396671
12e
ENSE00001642867
chr3:
24193981-24193881
101
THB_HUMAN
95-128
34
0
-
-
1.13b
ENST00000396671
13b
ENSE00001073518
chr3:
24188313-24188166
148
THB_HUMAN
129-178
50
0
-
-
1.14
ENST00000396671
14
ENSE00001073519
chr3:
24185197-24184992
206
THB_HUMAN
178-246
69
1
A:201-246
46
1.15
ENST00000396671
15
ENSE00001073517
chr3:
24174953-24174807
147
THB_HUMAN
247-295
49
1
A:247-295 (gaps)
49
1.16
ENST00000396671
16
ENSE00001718132
chr3:
24169248-24168990
259
THB_HUMAN
296-382
87
1
A:296-382
87
1.17d
ENST00000396671
17d
ENSE00001406950
chr3:
24164616-24158651
5966
THB_HUMAN
382-461
80
1
A:382-461
80
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d3imya_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All alpha proteins
(14657)
Fold
:
Nuclear receptor ligand-binding domain
(609)
Superfamily
:
Nuclear receptor ligand-binding domain
(609)
Family
:
Nuclear receptor ligand-binding domain
(598)
Protein domain
:
Thyroid hormone receptor beta (TR-beta)
(15)
Human (Homo sapiens) [TaxId: 9606]
(15)
1a
d3imya_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_3imyA00 (A:201-461)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Retinoid X Receptor
(409)
Homologous Superfamily
:
Retinoid X Receptor
(409)
Human (Homo sapiens)
(337)
1a
3imyA00
A:201-461
[
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 (48 KB)
Header - Asym.Unit
Biol.Unit 1 (44 KB)
Header - Biol.Unit 1
Biol.Unit 2 (85 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
3IMY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
