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.
1Y7N
Asym. Unit
Info
Asym.Unit (442 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
Models
(20 )
Title
:
SOLUTION STRUCTURE OF THE SECOND PDZ DOMAIN OF THE HUMAN NEURONAL ADAPTOR X11ALPHA
Authors
:
A. E. Duquesne, M. De Ruijter, J. Brouwer, J. W. Drijfhout, S. B. Nabuurs, C. A. E. M. Spronk, G. W. Vuister, M. Ubbink, G. W. Canters
Date
:
09 Dec 04 (Deposition) - 22 Nov 05 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A (20 x)
Keywords
:
Copper Chaperone For Superoxide Dismutase, Neuronal Adaptor, Protein Transport
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. E. Duquesne, M. De Ruijter, J. Brouwer, J. W. Drijfhout, S. B. Nabuurs, C. A. E. M. Spronk, G. W. Vuister, M. Ubbink, G. W. Canters
Solution Structure Of The Second Pdz Domain Of The Neuronal Adaptor X11Alpha And Its Interaction With The C-Terminal Peptide Of The Human Copper Chaperone For Superoxide Dismutase
J. Biomol. Nmr V. 32 209 2005
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available in "Model" view)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: PDZ (-|A:14-90)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
PDZ
PS50106
PDZ domain profile.
APBA1_HUMAN
656-741
747-823
1
-
A:14-90
[
close PROSITE info
]
Exons
(4, 4)
Info
All Exons
Exon 1.10 (A:7-11 (gaps))
Exon 1.11 (A:12-34)
Exon 1.12 (A:35-81)
Exon 1.13 (A:82-90)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.9/1.10
2: Boundary 1.10/1.11
3: Boundary 1.11/1.12
4: Boundary 1.12/1.13
5: Boundary 1.13/-
View:
Label:
Note:
Exon boundaries colored in "red" are actually farther away from the residue due to missing residues in the structure.
ENSEMBL
UniProtKB
PDB
No.
Transcript ID
Exon
Exon ID
Genome Location
Length
ID
Location
Length
Count
Location
Length
1.1
ENST00000265381
1
ENSE00001228144
chr9:
72287222-72287069
154
APBA1_HUMAN
-
0
0
-
-
1.2
ENST00000265381
2
ENSE00001089894
chr9:
72132195-72130927
1269
APBA1_HUMAN
1-400
400
0
-
-
1.3
ENST00000265381
3
ENSE00001089895
chr9:
72091059-72090964
96
APBA1_HUMAN
401-432
32
0
-
-
1.4
ENST00000265381
4
ENSE00001089892
chr9:
72086611-72086572
40
APBA1_HUMAN
433-446
14
0
-
-
1.5a
ENST00000265381
5a
ENSE00000982740
chr9:
72082884-72082739
146
APBA1_HUMAN
446-494
49
0
-
-
1.6
ENST00000265381
6
ENSE00001015445
chr9:
72073104-72073072
33
APBA1_HUMAN
495-505
11
0
-
-
1.7
ENST00000265381
7
ENSE00000982741
chr9:
72072055-72071969
87
APBA1_HUMAN
506-534
29
0
-
-
1.8b
ENST00000265381
8b
ENSE00000917481
chr9:
72071348-72071163
186
APBA1_HUMAN
535-596
62
0
-
-
1.9
ENST00000265381
9
ENSE00000982742
chr9:
72067217-72067038
180
APBA1_HUMAN
597-656
60
0
-
-
1.10
ENST00000265381
10
ENSE00000982743
chr9:
72064712-72064500
213
APBA1_HUMAN
657-727
71
1
A:7-11 (gaps)
7
1.11
ENST00000265381
11
ENSE00000982744
chr9:
72056031-72055912
120
APBA1_HUMAN
728-767
40
1
A:12-34
23
1.12
ENST00000265381
12
ENSE00000982745
chr9:
72047592-72047452
141
APBA1_HUMAN
768-814
47
1
A:35-81
47
1.13
ENST00000265381
13
ENSE00001228156
chr9:
72046314-72045204
1111
APBA1_HUMAN
815-837
23
1
A:82-90
9
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1y7na1 (A:12-90)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
PDZ domain-like
(299)
Superfamily
:
PDZ domain-like
(299)
Family
:
PDZ domain
(180)
Protein domain
:
Amyloid beta A4 precursor protein-binding family A member 1 (APBA1, X11)
(6)
Human (Homo sapiens) [TaxId: 9606]
(6)
1a
d1y7na1
A:12-90
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1y7nA00 (A:7-90)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Roll
(1513)
Topology
:
Pdz3 Domain
(191)
Homologous Superfamily
:
[code=2.30.42.10, no name defined]
(191)
Human (Homo sapiens)
(120)
1a
1y7nA00
A:7-90
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_PDZ_1y7nA01 (A:14-87)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
PDZ-like
(184)
Family
:
PDZ
(172)
Homo sapiens (Human)
(96)
1a
PDZ-1y7nA01
A:14-87
[
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
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 (442 KB)
Header - Asym.Unit
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
1Y7N
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
