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.
1M5F
Biol. Unit 3
Info
Asym.Unit (148 KB)
Biol.Unit 1 (95 KB)
Biol.Unit 2 (99 KB)
Biol.Unit 3 (142 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-Y702F) IN COMPLEX WITH ACPA AT 1.95 A RESOLUTION
Authors
:
A. Hogner, J. S. Kastrup, R. Jin, T. Liljefors, M. L. Mayer, J. Egebjerg, I. K. Larsen, E. Gouaux
Date
:
09 Jul 02 (Deposition) - 18 Sep 02 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.95
Chains
:
Asym. Unit : A,B,C
Biol. Unit 1: A,C (1x)
Biol. Unit 2: B (2x)
Biol. Unit 3: A,B,C (1x)
Keywords
:
Ionotrpoic Glutamate Receptor, Glur2, Ligand Binding Core, Agonist Complex. , Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Hogner, J. S. Kastrup, R. Jin, T. Liljefors, M. L. Mayer, J. Egebjerg, I. K. Larsen, E. Gouaux
Structural Basis For Ampa Receptor Activation And Ligand Selectivity: Crystal Structures Of Five Agonist Complexes With The Glur2 Ligand-Binding Core
J. Mol. Biol. V. 322 93 2002
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
2a: (S)-2-AMINO-3-(3-CARBOXY-5-METHYLI... (AM1a)
2b: (S)-2-AMINO-3-(3-CARBOXY-5-METHYLI... (AM1b)
2c: (S)-2-AMINO-3-(3-CARBOXY-5-METHYLI... (AM1c)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(10, 10)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
LYS A:45 , LYS B:144 , PHE B:170 , ZN B:1209 , HOH B:1216
BINDING SITE FOR RESIDUE ACT B 1203
02
AC2
SOFTWARE
HIS A:23 , HOH A:1420 , ASP C:65 , HOH C:1463
BINDING SITE FOR RESIDUE ZN A 1204
03
AC3
SOFTWARE
GLU A:42 , HIS A:46 , GLU B:166 , ZN B:1209
BINDING SITE FOR RESIDUE ZN B 1205
04
AC4
SOFTWARE
HIS B:23 , GLU B:30 , HIS C:23 , GLU C:24
BINDING SITE FOR RESIDUE ZN B 1206
05
AC5
SOFTWARE
GLU A:166 , GLU B:42 , LYS B:45 , HIS B:46 , LEU B:241 , HOH B:1529
BINDING SITE FOR RESIDUE ZN B 1207
06
AC6
SOFTWARE
GLU C:42 , LYS C:45 , HIS C:46
BINDING SITE FOR RESIDUE ZN C 1208
07
AC7
SOFTWARE
ACT B:1203 , ZN B:1205 , HOH B:1342
BINDING SITE FOR RESIDUE ZN B 1209
08
AC8
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 , LEU A:192 , GLU A:193 , MET A:196 , TYR A:220 , HOH A:1230 , HOH A:1254
BINDING SITE FOR RESIDUE AM1 A 1200
09
AC9
SOFTWARE
TYR B:61 , PRO B:89 , LEU B:90 , THR B:91 , ARG B:96 , GLY B:141 , SER B:142 , THR B:143 , LEU B:192 , GLU B:193 , MET B:196 , TYR B:220 , HOH B:1254 , HOH B:1280
BINDING SITE FOR RESIDUE AM1 B 1201
10
BC1
SOFTWARE
TYR C:61 , PRO C:89 , LEU C:90 , THR C:91 , ARG C:96 , GLY C:141 , SER C:142 , THR C:143 , LEU C:192 , GLU C:193 , MET C:196 , TYR C:220 , HOH C:1245 , HOH C:1255
BINDING SITE FOR RESIDUE AM1 C 1202
[
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_d1m5fa_ (A:)
1b: SCOP_d1m5fb_ (B:)
1c: SCOP_d1m5fc_ (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
d1m5fa_
A:
1b
d1m5fb_
B:
1c
d1m5fc_
C:
[
close SCOP info
]
CATH Domains
(1, 6)
Info
all CATH domains
1a: CATH_1m5fA02 (A:4-109,A:219-258)
1b: CATH_1m5fB02 (B:4-109,B:219-258)
1c: CATH_1m5fC02 (C:4-109,C:219-258)
1d: CATH_1m5fA01 (A:110-218)
1e: CATH_1m5fB01 (B:110-218)
1f: CATH_1m5fC01 (C: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
1m5fA02
A:4-109,A:219-258
1b
1m5fB02
B:4-109,B:219-258
1c
1m5fC02
C:4-109,C:219-258
1d
1m5fA01
A:110-218
1e
1m5fB01
B:110-218
1f
1m5fC01
C:110-218
[
close CATH info
]
Pfam Domains
(2, 6)
Info
all PFAM domains
1a: PFAM_Lig_chan_1m5fC01 (C:119-261)
1b: PFAM_Lig_chan_1m5fC02 (C:119-261)
1c: PFAM_Lig_chan_1m5fC03 (C:119-261)
2a: PFAM_Lig_chan_Glu_bd_1m5fC04 (C:15-80)
2b: PFAM_Lig_chan_Glu_bd_1m5fC05 (C:15-80)
2c: PFAM_Lig_chan_Glu_bd_1m5fC06 (C:15-80)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ion_channel
(150)
Family
:
Lig_chan
(109)
Rattus norvegicus (Rat)
(101)
1a
Lig_chan-1m5fC01
C:119-261
1b
Lig_chan-1m5fC02
C:119-261
1c
Lig_chan-1m5fC03
C:119-261
Clan
:
PBP
(391)
Family
:
Lig_chan-Glu_bd
(91)
Rattus norvegicus (Rat)
(86)
2a
Lig_chan-Glu_bd-1m5fC04
C:15-80
2b
Lig_chan-Glu_bd-1m5fC05
C:15-80
2c
Lig_chan-Glu_bd-1m5fC06
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 B
Chain C
Asymmetric Unit 1
Asymmetric Unit 2
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 (99 KB)
Header - Biol.Unit 2
Biol.Unit 3 (142 KB)
Header - Biol.Unit 3
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
1M5F
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
