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.
4IL4
Asym. Unit
Info
Asym.Unit (268 KB)
Biol.Unit 1 (262 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE PENTAMERIC LIGAND-GATED ION CHANNEL GLIC IN COMPLEX WITH SE-DDM
Authors
:
L. Sauguet, L. Malherbe, P. J. Corringer, M. Delarue
Date
:
29 Dec 12 (Deposition) - 20 Feb 13 (Release) - 20 Mar 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.30
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Pentameric Ligand-Gated Ion Channel, Ion Channel, Membrane, Membrane Protein, Transport Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Sauguet, F. Poitevin, S. Murail, C. Van Renterghem, G. Moraga-Cid L. Malherbe, A. W. Thompson, P. Koehl, P. J. Corringer, M. Baaden, M. Delarue
Structural Basis For Ion Permeation Mechanism In Pentameric Ligand-Gated Ion Channels.
Embo J. V. 32 728 2013
[
close entry info
]
Hetero Components
(4, 29)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
1c: ACETATE ION (ACTc)
1d: ACETATE ION (ACTd)
1e: ACETATE ION (ACTe)
1f: ACETATE ION (ACTf)
1g: ACETATE ION (ACTg)
1h: ACETATE ION (ACTh)
1i: ACETATE ION (ACTi)
1j: ACETATE ION (ACTj)
2a: CHLORIDE ION (CLa)
2b: CHLORIDE ION (CLb)
2c: CHLORIDE ION (CLc)
2d: CHLORIDE ION (CLd)
2e: CHLORIDE ION (CLe)
2f: CHLORIDE ION (CLf)
2g: CHLORIDE ION (CLg)
3a: DODECYL 4-O-ALPHA-D-GLUCOPYRANOSYL... (LSMa)
3b: DODECYL 4-O-ALPHA-D-GLUCOPYRANOSYL... (LSMb)
3c: DODECYL 4-O-ALPHA-D-GLUCOPYRANOSYL... (LSMc)
3d: DODECYL 4-O-ALPHA-D-GLUCOPYRANOSYL... (LSMd)
3e: DODECYL 4-O-ALPHA-D-GLUCOPYRANOSYL... (LSMe)
3f: DODECYL 4-O-ALPHA-D-GLUCOPYRANOSYL... (LSMf)
4a: SODIUM ION (NAa)
4b: SODIUM ION (NAb)
4c: SODIUM ION (NAc)
4d: SODIUM ION (NAd)
4e: SODIUM ION (NAe)
4f: SODIUM ION (NAf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
10
Ligand/Ion
ACETATE ION
2
CL
7
Ligand/Ion
CHLORIDE ION
3
LSM
6
Ligand/Ion
DODECYL 4-O-ALPHA-D-GLUCOPYRANOSYL-1-SELENO-BETA-D-GLUCOPYRANOSIDE
4
NA
6
Ligand/Ion
SODIUM ION
[
close Hetero Component info
]
Sites
(28, 28)
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)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:77 , ILE A:131 , GLU A:181 , PHE E:42 , ARG E:105
BINDING SITE FOR RESIDUE ACT A 401
02
AC2
SOFTWARE
PHE A:78 , ARG A:85
BINDING SITE FOR RESIDUE CL A 402
03
AC3
SOFTWARE
ASN A:139 , LEU A:180 , ALA D:175
BINDING SITE FOR RESIDUE CL A 403
04
AC4
SOFTWARE
ALA A:175 , ASN D:139 , LEU D:180
BINDING SITE FOR RESIDUE CL A 404
05
AC5
SOFTWARE
PRO A:68 , ILE A:71 , ILE A:73
BINDING SITE FOR RESIDUE NA A 405
06
AC6
SOFTWARE
ILE A:73 , PRO A:74 , ILE A:76 , ARG A:85 , TYR A:102
BINDING SITE FOR RESIDUE ACT A 407
07
AC7
SOFTWARE
ALA A:237 , ALA E:237
BINDING SITE FOR RESIDUE LSM A 408
08
AC8
SOFTWARE
PHE A:42 , ARG A:105 , ARG B:77 , ILE B:131 , GLU B:181
BINDING SITE FOR RESIDUE ACT B 401
09
AC9
SOFTWARE
PHE B:78 , ARG B:85
BINDING SITE FOR RESIDUE CL B 402
10
BC1
SOFTWARE
PRO B:68 , ILE B:71 , TRP B:72 , ILE B:73
BINDING SITE FOR RESIDUE NA B 403
11
BC2
SOFTWARE
ILE B:73 , PRO B:74 , ILE B:76 , ARG B:85 , TYR B:102
BINDING SITE FOR RESIDUE ACT B 404
12
BC3
SOFTWARE
ALA A:237 , ALA B:237
BINDING SITE FOR RESIDUE LSM B 405
13
BC4
SOFTWARE
PHE B:42 , ARG B:105 , ARG C:77 , ILE C:131 , GLU C:181
BINDING SITE FOR RESIDUE ACT C 401
14
BC5
SOFTWARE
PHE C:78 , ARG C:85
BINDING SITE FOR RESIDUE CL C 402
15
BC6
SOFTWARE
PRO C:68 , ILE C:71 , ILE C:73
BINDING SITE FOR RESIDUE NA C 403
16
BC7
SOFTWARE
ILE C:73 , PRO C:74 , ILE C:76 , ARG C:85 , TYR C:102
BINDING SITE FOR RESIDUE ACT C 404
17
BC8
SOFTWARE
LSM D:406
BINDING SITE FOR RESIDUE LSM C 405
18
BC9
SOFTWARE
PHE C:42 , ARG C:105 , ARG D:77 , ILE D:131 , GLU D:181
BINDING SITE FOR RESIDUE ACT D 401
19
CC1
SOFTWARE
PHE D:78 , ARG D:85
BINDING SITE FOR RESIDUE CL D 402
20
CC2
SOFTWARE
VAL D:5 , ILE D:71 , ILE D:73
BINDING SITE FOR RESIDUE NA D 403
21
CC3
SOFTWARE
ILE D:73 , PRO D:74 , ILE D:76 , ARG D:85 , TYR D:102
BINDING SITE FOR RESIDUE ACT D 404
22
CC4
SOFTWARE
ILE D:233 , ALA D:237 , ILE D:240 , THR D:244
BINDING SITE FOR RESIDUE LSM D 405
23
CC5
SOFTWARE
LSM C:405 , LSM E:405
BINDING SITE FOR RESIDUE LSM D 406
24
CC6
SOFTWARE
PHE D:42 , ARG D:105 , ARG E:77 , ILE E:131 , GLU E:181
BINDING SITE FOR RESIDUE ACT E 401
25
CC7
SOFTWARE
PHE E:78 , ARG E:85
BINDING SITE FOR RESIDUE CL E 402
26
CC8
SOFTWARE
PRO E:68 , ILE E:71 , ILE E:73
BINDING SITE FOR RESIDUE NA E 403
27
CC9
SOFTWARE
PRO E:74 , ILE E:76 , ARG E:85 , TYR E:102
BINDING SITE FOR RESIDUE ACT E 404
28
DC1
SOFTWARE
LSM D:406 , ILE E:240
BINDING SITE FOR RESIDUE LSM E 405
[
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
(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
Chain E
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 (268 KB)
Header - Asym.Unit
Biol.Unit 1 (262 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
4IL4
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
