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.
2Y31
Asym. Unit
Info
Asym.Unit (93 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
:
SIMOCYCLINONE C4 BOUND FORM OF TETR-LIKE REPRESSOR SIMR
Authors
:
T. B. K. Le, C. E. M. Stevenson, H. -P. Fiedler, A. Maxwell, D. M. Lawson, M. J. Buttner
Date
:
17 Dec 10 (Deposition) - 09 Mar 11 (Release) - 25 May 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Transcription, Tetr-Family
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. B. K. Le, C. E. M. Stevenson, H. -P. Fiedler, A. Maxwell, D. M. Lawson, M. J. Buttner
Structures Of The Tetr-Like Simocyclinone Efflux Pump Repressor, Simr, And The Mechanism Of Ligand- Mediated Derepression.
J. Mol. Biol. V. 408 40 2011
[
close entry info
]
Hetero Components
(5, 13)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
2a: CALCIUM ION (CAa)
3a: CHLORIDE ION (CLa)
3b: CHLORIDE ION (CLb)
3c: CHLORIDE ION (CLc)
3d: CHLORIDE ION (CLd)
3e: CHLORIDE ION (CLe)
3f: CHLORIDE ION (CLf)
3g: CHLORIDE ION (CLg)
3h: CHLORIDE ION (CLh)
4a: TETRAETHYLENE GLYCOL (PG4a)
5a: SIMOCYCLINONE C4 (SMQa)
5b: SIMOCYCLINONE C4 (SMQb)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
1
Ligand/Ion
PENTAETHYLENE GLYCOL
2
CA
1
Ligand/Ion
CALCIUM ION
3
CL
8
Ligand/Ion
CHLORIDE ION
4
PG4
1
Ligand/Ion
TETRAETHYLENE GLYCOL
5
SMQ
2
Ligand/Ion
SIMOCYCLINONE C4
[
close Hetero Component info
]
Sites
(13, 13)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
MET A:185 , MET A:189 , GLY A:193 , GLN A:197 , LEU A:212 , HIS A:219 , HOH A:2140 , HOH A:2166 , HOH A:2168 , PRO B:126 , GLN B:135 , GLN B:136 , LEU B:154 , ASN B:161 , HOH B:2057
BINDING SITE FOR RESIDUE SMQ A 501
02
AC2
SOFTWARE
LYS A:107 , PRO A:126 , GLN A:135 , GLN A:136 , LEU A:154 , ASN A:161 , HOH A:2097 , MET B:189 , GLY B:193 , GLN B:197 , LEU B:212 , PRO B:218 , HIS B:219 , HOH B:2099
BINDING SITE FOR RESIDUE SMQ B 501
03
AC3
SOFTWARE
ARG A:232 , ASP A:235 , SER A:236 , HOH A:2159 , HOH A:2169 , SER B:240 , ARG B:243 , LEU B:244
BINDING SITE FOR RESIDUE 1PE A1248
04
AC4
SOFTWARE
LEU A:88 , PRO A:89 , ASP A:90 , ARG A:134 , GLU A:137 , PHE A:138 , HOH A:2045
BINDING SITE FOR RESIDUE PG4 A1249
05
AC5
SOFTWARE
LEU A:244 , HOH A:2088 , HOH A:2090 , ASP B:235 , HOH B:2040 , HOH B:2041
BINDING SITE FOR RESIDUE CA B1247
06
AC6
SOFTWARE
HOH A:2073 , GLY B:44 , VAL B:45 , TRP B:116 , HOH B:2018 , HOH B:2053
BINDING SITE FOR RESIDUE CL B1248
07
AC7
SOFTWARE
LYS B:71 , HOH B:2024
BINDING SITE FOR RESIDUE CL B1249
08
AC8
SOFTWARE
MET B:185 , HOH B:2092
BINDING SITE FOR RESIDUE CL B1250
09
AC9
SOFTWARE
TRP A:174 , ASP A:184 , MET A:185 , HOH A:2106 , HOH A:2120
BINDING SITE FOR RESIDUE CL A1250
10
BC1
SOFTWARE
MET B:50 , HOH B:2020 , HOH B:2024
BINDING SITE FOR RESIDUE CL B1251
11
BC2
SOFTWARE
GLY A:44 , VAL A:45 , HOH A:2018 , HOH B:2056
BINDING SITE FOR RESIDUE CL A1251
12
BC3
SOFTWARE
GLY B:221 , ASP B:223 , GLN B:224
BINDING SITE FOR RESIDUE CL B1252
13
BC4
SOFTWARE
GLY A:221 , ASP A:223 , GLN A:224 , HOH A:2145
BINDING SITE FOR RESIDUE CL A1252
[
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
(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.
SCOP Domains
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 4)
Info
all PFAM domains
1a: PFAM_TetR_N_2y31B01 (B:32-78)
1b: PFAM_TetR_N_2y31B02 (B:32-78)
2a: PFAM_TetR_C_2y31B03 (B:88-241)
2b: PFAM_TetR_C_2y31B04 (B:88-241)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
HTH
(544)
Family
:
TetR_N
(84)
Streptomyces antibioticus
(3)
1a
TetR_N-2y31B01
B:32-78
1b
TetR_N-2y31B02
B:32-78
Clan
:
TetR_C
(33)
Family
:
TetR_C
(16)
Streptomyces antibioticus
(3)
2a
TetR_C-2y31B03
B:88-241
2b
TetR_C-2y31B04
B:88-241
[
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 (93 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
2Y31
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
