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.
1N0T
Biol. Unit 2
Info
Asym.Unit (190 KB)
Biol.Unit 1 (95 KB)
Biol.Unit 2 (94 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
X-RAY STRUCTURE OF THE GLUR2 LIGAND-BINDING CORE (S1S2J) IN COMPLEX WITH THE ANTAGONIST (S)-ATPO AT 2.1 A RESOLUTION.
Authors
:
A. Hogner, J. R. Greenwood, T. Liljefors, M. -L. Lunn, J. Egebjerg, I. K. E. Gouaux, J. S. Kastrup
Date
:
15 Oct 02 (Deposition) - 04 Mar 03 (Release) - 21 Dec 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.10
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B,D (1x)
Keywords
:
Ionotropic Glutamate Receptor Glur2, Ligand-Binding Core, Antagonist Complex, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Hogner, J. R. Greenwood, T. Liljefors, M. L. Lunn, J. Egebjerg, I. K. Larsen, E. Gouaux, J. S. Kastrup
Competitive Antagonism Of Ampa Receptors By Ligands Of Different Classes: Crystal Structure Of Atpo Bound To The Glur2 Ligand-Binding Core, In Comparison With Dnqx.
J. Med. Chem. V. 46 214 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(3, 5)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: (S)-2-AMINO-3-(5-TERT-BUTYL-3-(PHO... (AT1a)
2b: (S)-2-AMINO-3-(5-TERT-BUTYL-3-(PHO... (AT1b)
2c: (S)-2-AMINO-3-(5-TERT-BUTYL-3-(PHO... (AT1c)
2d: (S)-2-AMINO-3-(5-TERT-BUTYL-3-(PHO... (AT1d)
3a: SULFATE ION (SO4a)
3b: SULFATE ION (SO4b)
3c: SULFATE ION (SO4c)
3d: SULFATE ION (SO4d)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
1
Ligand/Ion
ACETATE ION
2
AT1
2
Ligand/Ion
(S)-2-AMINO-3-(5-TERT-BUTYL-3-(PHOSPHONOMETHOXY)-4-ISOXAZOLYL)PROPIONIC ACID
3
SO4
2
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(5, 5)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC5 (SOFTWARE)
4: AC7 (SOFTWARE)
5: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
LYS B:144 , ARG B:148 , ARG B:163 , HOH B:377 , HIS D:23
BINDING SITE FOR RESIDUE SO4 B 264
2
AC3
SOFTWARE
HIS B:23 , LYS D:144 , ARG D:148 , ARG D:163 , HOH D:424 , HOH D:464
BINDING SITE FOR RESIDUE SO4 D 264
3
AC5
SOFTWARE
THR D:174 , HOH D:476 , HOH D:477
BINDING SITE FOR RESIDUE ACT D 265
4
AC7
SOFTWARE
GLU B:13 , TYR B:61 , PRO B:89 , LEU B:90 , THR B:91 , ARG B:96 , GLY B:141 , SER B:142 , THR B:143 , GLU B:193 , THR B:195 , TYR B:220 , HOH B:267 , HOH B:294 , HOH B:306 , HOH B:380 , HOH B:384 , HOH B:446
BINDING SITE FOR RESIDUE AT1 B 265
5
AC9
SOFTWARE
GLU D:13 , TYR D:61 , PRO D:89 , LEU D:90 , THR D:91 , ARG D:96 , LEU D:138 , GLY D:141 , SER D:142 , THR D:143 , GLU D:193 , TYR D:220 , HOH D:273 , HOH D:295 , HOH D:308 , HOH D:335 , HOH D:341 , HOH D:495
BINDING SITE FOR RESIDUE AT1 D 266
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(, 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.
(no "Exon" information available for biological units yet)
SCOP Domains
(1, 4)
Info
All SCOP Domains
1a: SCOP_d1n0ta_ (A:)
1b: SCOP_d1n0tb_ (B:)
1c: SCOP_d1n0tc_ (C:)
1d: SCOP_d1n0td_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Periplasmic binding protein-like II
(813)
Superfamily
:
Periplasmic binding protein-like II
(813)
Family
:
Phosphate binding protein-like
(463)
Protein domain
:
Glutamate receptor ligand binding core
(127)
Norway rat (Rattus norvegicus), GluR2 [TaxId: 10116]
(115)
1a
d1n0ta_
A:
1b
d1n0tb_
B:
1c
d1n0tc_
C:
1d
d1n0td_
D:
[
close SCOP info
]
CATH Domains
(1, 8)
Info
all CATH domains
1a: CATH_1n0tA02 (A:5-109,A:219-258)
1b: CATH_1n0tB02 (B:5-109,B:219-258)
1c: CATH_1n0tC02 (C:5-109,C:219-258)
1d: CATH_1n0tD02 (D:5-109,D:219-258)
1e: CATH_1n0tA01 (A:110-218)
1f: CATH_1n0tB01 (B:110-218)
1g: CATH_1n0tC01 (C:110-218)
1h: CATH_1n0tD01 (D:110-218)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
D-Maltodextrin-Binding Protein; domain 2
(600)
Homologous Superfamily
:
Periplasmic binding protein-like II
(486)
Norway rat (Rattus norvegicus)
(84)
1a
1n0tA02
A:5-109,A:219-258
1b
1n0tB02
B:5-109,B:219-258
1c
1n0tC02
C:5-109,C:219-258
1d
1n0tD02
D:5-109,D:219-258
1e
1n0tA01
A:110-218
1f
1n0tB01
B:110-218
1g
1n0tC01
C:110-218
1h
1n0tD01
D:110-218
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_Lig_chan_1n0tD01 (D:120-261)
1b: PFAM_Lig_chan_1n0tD02 (D:120-261)
1c: PFAM_Lig_chan_1n0tD03 (D:120-261)
1d: PFAM_Lig_chan_1n0tD04 (D:120-261)
2a: PFAM_Lig_chan_Glu_bd_1n0tD05 (D:15-80)
2b: PFAM_Lig_chan_Glu_bd_1n0tD06 (D:15-80)
2c: PFAM_Lig_chan_Glu_bd_1n0tD07 (D:15-80)
2d: PFAM_Lig_chan_Glu_bd_1n0tD08 (D:15-80)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ion_channel
(150)
Family
:
Lig_chan
(109)
Rattus norvegicus (Rat)
(101)
1a
Lig_chan-1n0tD01
D:120-261
1b
Lig_chan-1n0tD02
D:120-261
1c
Lig_chan-1n0tD03
D:120-261
1d
Lig_chan-1n0tD04
D:120-261
Clan
:
PBP
(391)
Family
:
Lig_chan-Glu_bd
(91)
Rattus norvegicus (Rat)
(86)
2a
Lig_chan-Glu_bd-1n0tD05
D:15-80
2b
Lig_chan-Glu_bd-1n0tD06
D:15-80
2c
Lig_chan-Glu_bd-1n0tD07
D:15-80
2d
Lig_chan-Glu_bd-1n0tD08
D:15-80
[
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 B
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 (190 KB)
Header - Asym.Unit
Biol.Unit 1 (95 KB)
Header - Biol.Unit 1
Biol.Unit 2 (94 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
1N0T
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
