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.
5AFJ
Asym. Unit
Info
Asym.Unit (396 KB)
Biol.Unit 1 (385 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
ALPHA7-ACHBP IN COMPLEX WITH LOBELINE AND FRAGMENT 1
Authors
:
R. Spurny, S. Debaveye, A. Farinha, K. Veys, T. Gossas, J. Atack, D. Bert J. Kemp, A. Vos, U. H. Danielson, G. Tresadern, C. Ulens
Date
:
22 Jan 15 (Deposition) - 06 May 15 (Release) - 15 Mar 17 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E (1x)
Keywords
:
Transport Protein, Pentameric Ligand-Gated Ion Channels, Cys-Loop Receptor, Nicotinic Acetylcholine Receptor, Allosteric Modulation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
R. Spurny, S. Debaveye, A. Farinha, K. Veys, A. M. Vos, T. Gossas, J. Atack, S. Bertrand, D. Bertrand, U. H. Danielson, G. Tresadern, C. Ulens
Molecular Blueprint Of Allosteric Binding Sites In A Homologue Of The Agonist-Binding Domain Of The Alpha7 Nicotinic Acetylcholine Receptor.
Proc. Natl. Acad. Sci. Usa V. 112 E2543 2015
[
close entry info
]
Hetero Components
(6, 30)
Info
All Hetero Components
1a: (3S)-6-(4-BROMOPHENYL)-3-HYDROXY-1... (42Ra)
1b: (3S)-6-(4-BROMOPHENYL)-3-HYDROXY-1... (42Rb)
1c: (3S)-6-(4-BROMOPHENYL)-3-HYDROXY-1... (42Rc)
1d: (3S)-6-(4-BROMOPHENYL)-3-HYDROXY-1... (42Rd)
1e: (3S)-6-(4-BROMOPHENYL)-3-HYDROXY-1... (42Re)
1f: (3S)-6-(4-BROMOPHENYL)-3-HYDROXY-1... (42Rf)
1g: (3S)-6-(4-BROMOPHENYL)-3-HYDROXY-1... (42Rg)
1h: (3S)-6-(4-BROMOPHENYL)-3-HYDROXY-1... (42Rh)
1i: (3S)-6-(4-BROMOPHENYL)-3-HYDROXY-1... (42Ri)
1j: (3S)-6-(4-BROMOPHENYL)-3-HYDROXY-1... (42Rj)
2a: BETA-D-MANNOSE (BMAa)
3a: GLYCEROL (GOLa)
3b: GLYCEROL (GOLb)
3c: GLYCEROL (GOLc)
4a: ALPHA-LOBELINE (L0Ba)
4b: ALPHA-LOBELINE (L0Bb)
4c: ALPHA-LOBELINE (L0Bc)
4d: ALPHA-LOBELINE (L0Bd)
4e: ALPHA-LOBELINE (L0Be)
5a: ALPHA-D-MANNOSE (MANa)
6a: N-ACETYL-D-GLUCOSAMINE (NAGa)
6b: N-ACETYL-D-GLUCOSAMINE (NAGb)
6c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6d: N-ACETYL-D-GLUCOSAMINE (NAGd)
6e: N-ACETYL-D-GLUCOSAMINE (NAGe)
6f: N-ACETYL-D-GLUCOSAMINE (NAGf)
6g: N-ACETYL-D-GLUCOSAMINE (NAGg)
6h: N-ACETYL-D-GLUCOSAMINE (NAGh)
6i: N-ACETYL-D-GLUCOSAMINE (NAGi)
6j: N-ACETYL-D-GLUCOSAMINE (NAGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
42R
10
Ligand/Ion
(3S)-6-(4-BROMOPHENYL)-3-HYDROXY-1,3-DIMETHYL-2,3-DIHYDROPYRIDIN-4(1H)-ONE
2
BMA
1
Ligand/Ion
BETA-D-MANNOSE
3
GOL
3
Ligand/Ion
GLYCEROL
4
L0B
5
Ligand/Ion
ALPHA-LOBELINE
5
MAN
1
Ligand/Ion
ALPHA-D-MANNOSE
6
NAG
10
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(30, 30)
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)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:108 , SER A:109 , SER A:110 , HIS A:112 , NAG A:302
BINDING SITE FOR RESIDUE NAG A 301
02
AC2
SOFTWARE
NAG A:301
BINDING SITE FOR RESIDUE NAG A 302
03
AC3
SOFTWARE
ASN B:108 , SER B:110 , HIS B:112 , NAG B:302
BINDING SITE FOR RESIDUE NAG B 301
04
AC4
SOFTWARE
NAG B:301
BINDING SITE FOR RESIDUE NAG B 302
05
AC5
SOFTWARE
ASN C:108 , SER C:109 , SER C:110 , HIS C:112 , NAG C:302
BINDING SITE FOR RESIDUE NAG C 301
06
AC6
SOFTWARE
NAG C:301
BINDING SITE FOR RESIDUE NAG C 302
07
AC7
SOFTWARE
ASN D:108 , SER D:109 , SER D:110 , HIS D:112 , NAG D:302
BINDING SITE FOR RESIDUE NAG D 301
08
AC8
SOFTWARE
NAG D:301 , BMA D:303
BINDING SITE FOR RESIDUE NAG D 302
09
AC9
SOFTWARE
NAG D:302 , MAN D:304 , HOH D:2152
BINDING SITE FOR RESIDUE BMA D 303
10
BC1
SOFTWARE
BMA D:303 , HOH D:2153
BINDING SITE FOR RESIDUE MAN D 304
11
BC2
SOFTWARE
ASN E:108 , SER E:109 , SER E:110 , HIS E:112 , NAG E:302
BINDING SITE FOR RESIDUE NAG E 301
12
BC3
SOFTWARE
NAG E:301 , HOH E:2043
BINDING SITE FOR RESIDUE NAG E 302
13
BC4
SOFTWARE
LEU A:6 , GLU A:9 , LEU A:10 , ASN A:13 , LEU A:63 , GLN A:64 , TYR A:70
BINDING SITE FOR RESIDUE 42R A 1205
14
BC5
SOFTWARE
TYR A:91 , ASN A:92 , LYS A:141 , L0B A:1207 , HOH A:2135 , LEU B:36 , GLN B:37 , ILE B:165
BINDING SITE FOR RESIDUE 42R A 1206
15
BC6
SOFTWARE
TYR A:91 , TRP A:145 , CYS A:186 , CYS A:187 , TYR A:191 , 42R A:1206 , HOH A:2137 , TRP B:53 , GLN B:55 , GLN B:114 , LEU B:116
BINDING SITE FOR RESIDUE L0B A 1207
16
BC7
SOFTWARE
LEU B:6 , GLU B:9 , LEU B:10 , LEU B:63 , TRP B:65 , TYR B:70
BINDING SITE FOR RESIDUE 42R B 1205
17
BC8
SOFTWARE
TYR B:91 , ASN B:92 , ILE B:94 , LYS B:141 , TYR B:184 , L0B B:1207 , LEU C:36 , GLN C:37 , TRP C:53 , ILE C:165
BINDING SITE FOR RESIDUE 42R B 1206
18
BC9
SOFTWARE
TYR B:91 , TRP B:145 , THR B:146 , TYR B:184 , CYS B:186 , CYS B:187 , TYR B:191 , 42R B:1206 , HOH B:2093 , HOH B:2120 , TRP C:53 , LEU C:104 , LEU C:106 , GLN C:114 , LEU C:116 , HOH C:2032 , HOH C:2083
BINDING SITE FOR RESIDUE L0B B 1207
19
CC1
SOFTWARE
LEU C:6 , GLU C:9 , TYR C:62 , LEU C:63 , TRP C:65 , TYR C:70 , HOH C:2003 , HOH C:2055 , HOH E:2109
BINDING SITE FOR RESIDUE 42R C 1205
20
CC2
SOFTWARE
TYR C:91 , ASN C:92 , LYS C:141 , L0B C:1207 , HOH C:2096 , LEU D:36 , ILE D:165 , HOH D:2132
BINDING SITE FOR RESIDUE 42R C 1206
21
CC3
SOFTWARE
TYR C:91 , SER C:144 , TRP C:145 , CYS C:186 , TYR C:191 , 42R C:1206 , HOH C:2135 , TRP D:53 , GLN D:55 , GLN D:114 , LEU D:116 , HOH D:2109
BINDING SITE FOR RESIDUE L0B C 1207
22
CC4
SOFTWARE
LEU D:6 , GLU D:9 , ASN D:13 , TYR D:62 , LEU D:63 , TRP D:65 , TYR D:70 , VAL D:76
BINDING SITE FOR RESIDUE 42R D 1205
23
CC5
SOFTWARE
TYR D:91 , ASN D:92 , SER D:124 , LYS D:141 , L0B D:1207 , HOH D:2091 , ILE E:165 , HOH E:2091
BINDING SITE FOR RESIDUE 42R D 1206
24
CC6
SOFTWARE
TYR D:91 , TRP D:145 , CYS D:186 , CYS D:187 , TYR D:191 , 42R D:1206 , HOH D:2146 , LEU E:36 , TRP E:53 , GLN E:114 , HOH E:2078
BINDING SITE FOR RESIDUE L0B D 1207
25
CC7
SOFTWARE
LEU E:6 , GLU E:9 , LEU E:10 , ASN E:13 , TYR E:62 , LEU E:63 , TRP E:65 , TYR E:70
BINDING SITE FOR RESIDUE 42R E 1205
26
CC8
SOFTWARE
LEU A:36 , ILE A:165 , HOH A:2105 , TYR E:91 , ASN E:92 , LYS E:141 , ARG E:182 , TYR E:184 , L0B E:1207
BINDING SITE FOR RESIDUE 42R E 1206
27
CC9
SOFTWARE
LEU A:36 , TRP A:53 , GLN A:114 , LEU A:116 , TYR E:91 , SER E:144 , TRP E:145 , CYS E:186 , TYR E:191 , 42R E:1206 , HOH E:2103
BINDING SITE FOR RESIDUE L0B E 1207
28
DC1
SOFTWARE
MET C:56 , LEU C:88 , TYR C:115 , HOH C:2085
BINDING SITE FOR RESIDUE GOL C 1208
29
DC2
SOFTWARE
LEU D:88 , GLN D:121
BINDING SITE FOR RESIDUE GOL D 1208
30
DC3
SOFTWARE
LEU E:54 , PRO E:97 , GLN E:121 , PHE E:142 , HOH E:2064 , HOH E:2065
BINDING SITE FOR RESIDUE GOL E 1208
[
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 (396 KB)
Header - Asym.Unit
Biol.Unit 1 (385 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
5AFJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help