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.
2XXI
Biol. Unit 1
Info
Asym.Unit (148 KB)
Biol.Unit 1 (95 KB)
Biol.Unit 2 (97 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
CRYSTAL STRUCTURE OF 1-((4-(3-(TRIFLUOROMETHYL)-6,7-DIHYDROPYRANO(4,3 -C(PYRAZOL-1(4H)-YL)PHENYL)METHYL)-2-PYRROLIDINONE IN COMPLEX WITH THE LIGAND BINDING DOMAIN OF THE RAT GLUA2 RECEPTOR AND GLUTAMATE AT 1.6A RESOLUTION.
Authors
:
S. E. Ward, M. Harries, L. Aldegheri, N. E. Austin, S. Ballantine, E. Bal D. M. Bradley, B. D. Bax, B. P. Clarke, A. J. Harris, S. A. Harrison, R. A. Melarange, C. Mookherjee, J. Mosley, G. Dalnegro, B. Oliosi, K. J K. M. Thewlis, P. M. Woollard, S. P. Yusaf
Date
:
10 Nov 10 (Deposition) - 06 Apr 11 (Release) - 28 Sep 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.60
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B (2x)
Keywords
:
Transport Protein, Ampa Receptor Ligand-Binding Core, Ion Channel
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. E. Ward, M. Harries, L. Aldegheri, N. E. Austin, S. Ballantine, E. Ballini, D. M. Bradley, B. D. Bax, B. P. Clarke, A. J. Harris, S. A. Harrison, R. A. Melarange, C. Mookherjee, J. Mosley, G. Dal Negro, B. Oliosi, K. J. Smith, K. M. Thewlis, P. M. Woollard, S. P. Yusaf
Integration Of Lead Optimization With Crystallography For A Membrane-Bound Ion Channel Target: Discovery Of A New Class Of Ampa Receptor Positive Allosteric Modulators.
J. Med. Chem. V. 54 78 2011
[
close entry info
]
Hetero Components
(3, 4)
Info
All Hetero Components
1a: GLUTAMIC ACID (GLUa)
1b: GLUTAMIC ACID (GLUb)
1c: GLUTAMIC ACID (GLUc)
2a: 1-({4-[3-(TRIFLUOROMETHYL)-6,7-DIH... (JACa)
2b: 1-({4-[3-(TRIFLUOROMETHYL)-6,7-DIH... (JACb)
3a: SULFATE ION (SO4a)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
4e: ZINC ION (ZNe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GLU
2
Mod. Amino Acid
GLUTAMIC ACID
2
JAC
1
Ligand/Ion
1-({4-[3-(TRIFLUOROMETHYL)-6,7-DIHYDROPYRANO[4,3-C]PYRAZOL-1(4H)-YL]PHENYL}METHYL)-2-PYRROLIDINONE
3
SO4
1
Ligand/Ion
SULFATE ION
4
ZN
-1
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC3 (SOFTWARE)
3: AC4 (SOFTWARE)
4: AC6 (SOFTWARE)
5: AC7 (SOFTWARE)
6: AC8 (SOFTWARE)
7: AC9 (SOFTWARE)
8: BC1 (SOFTWARE)
9: BC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
TYR A:61 , PRO A:89 , LEU A:90 , THR A:91 , ARG A:96 , GLY A:141 , SER A:142 , THR A:143 , GLU A:193 , HOH A:2122 , HOH A:2171 , HOH A:2172
BINDING SITE FOR RESIDUE GLU A 301
2
AC3
SOFTWARE
TYR C:61 , PRO C:89 , LEU C:90 , THR C:91 , ARG C:96 , LEU C:138 , GLY C:141 , SER C:142 , THR C:143 , GLU C:193 , HOH C:2087 , HOH C:2117 , HOH C:2154
BINDING SITE FOR RESIDUE GLU C 301
3
AC4
SOFTWARE
ILE A:92 , LYS A:104 , PRO A:105 , PHE A:106 , MET A:107 , SER A:108 , SER A:217 , LYS A:218 , GLY A:219 , LEU A:239 , SER A:242 , HOH A:2022 , HOH A:2066 , HOH A:2074 , HOH A:2076 , HOH A:2151 , HOH A:2173 , HOH A:2174 , HOH A:2175 , HOH A:2176 , ILE C:92 , LYS C:104 , PRO C:105 , PHE C:106 , SER C:108 , SER C:217 , LYS C:218 , GLY C:219 , LEU C:239 , SER C:242 , HOH C:2063 , HOH C:2072 , HOH C:2076
BINDING SITE FOR RESIDUE JAC A1302
4
AC6
SOFTWARE
GLU A:42 , LYS A:45 , HIS A:46 , ZN A:1305 , ARG B:163 , ALA B:165 , GLU B:166 , SER B:168
BINDING SITE FOR RESIDUE SO4 A1304
5
AC7
SOFTWARE
GLU A:42 , HIS A:46 , SO4 A:1304 , GLU B:166
BINDING SITE FOR RESIDUE ZN A1305
6
AC8
SOFTWARE
HIS B:23 , GLU B:30 , HIS C:23 , GLU C:24
BINDING SITE FOR RESIDUE ZN B1303
7
AC9
SOFTWARE
HIS A:23 , ASP C:65 , HOH C:2155 , HOH C:2156
BINDING SITE FOR RESIDUE ZN C1302
8
BC1
SOFTWARE
GLU A:166 , GLU B:42 , HIS B:46 , LEU B:241 , HOH B:2188
BINDING SITE FOR RESIDUE ZN B1304
9
BC2
SOFTWARE
GLU C:42 , LYS C:45 , HIS C:46 , HOH C:2157 , HOH C:2158
BINDING SITE FOR RESIDUE ZN C1303
[
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, 3)
Info
All SCOP Domains
1a: SCOP_d2xxia_ (A:)
1b: SCOP_d2xxib_ (B:)
1c: SCOP_d2xxic_ (C:)
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
d2xxia_
A:
1b
d2xxib_
B:
1c
d2xxic_
C:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Lig_chan_2xxiC01 (C:120-301)
1b: PFAM_Lig_chan_2xxiC02 (C:120-301)
1c: PFAM_Lig_chan_2xxiC03 (C:120-301)
2a: PFAM_Lig_chan_Glu_bd_2xxiC04 (C:15-80)
2b: PFAM_Lig_chan_Glu_bd_2xxiC05 (C:15-80)
2c: PFAM_Lig_chan_Glu_bd_2xxiC06 (C:15-80)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ion_channel
(150)
Family
:
Lig_chan
(109)
Rattus norvegicus (Rat)
(101)
1a
Lig_chan-2xxiC01
C:120-301
1b
Lig_chan-2xxiC02
C:120-301
1c
Lig_chan-2xxiC03
C:120-301
Clan
:
PBP
(391)
Family
:
Lig_chan-Glu_bd
(91)
Rattus norvegicus (Rat)
(86)
2a
Lig_chan-Glu_bd-2xxiC04
C:15-80
2b
Lig_chan-Glu_bd-2xxiC05
C:15-80
2c
Lig_chan-Glu_bd-2xxiC06
C: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 A
Chain C
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 (148 KB)
Header - Asym.Unit
Biol.Unit 1 (95 KB)
Header - Biol.Unit 1
Biol.Unit 2 (97 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
2XXI
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
