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.
1NMJ
Asym. Unit
Info
Asym.Unit (10 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
THE SOLUTION STRUCTURE OF RAT AB-(1-28) AND ITS INTERACTION WITH ZINC: INSIGHTS INTO THE SCARITY OF AMYLOID DEPOSITION IN AGED RAT BRAIN
Authors
:
J. Huang, Y. Yao, W. X. Tang
Date
:
10 Jan 03 (Deposition) - 28 Jan 03 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A
Keywords
:
Glycoprotein, Amyloid, Membrane Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Huang, Y. Yao, J. Lin, Y. H. Ye, W. Y. Sun, W. X. Tang
The Solution Structure Of Rat Abeta-(1-28) And Its Interaction With Zinc Ion: Insights Into The Scarcity Of Amyloid Deposition In Aged Rat Brain
J. Biol. Inorg. Chem. V. 9 627 2004
(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)
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
(2, 2)
Info
All Exons
Exon 1.17 (A:1-17)
Exon 1.18 (A:18-28)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.16/1.17
2: Boundary 1.17/1.18
3: Boundary 1.18/1.19a
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
1.1b
ENSRNOT00000048854
1b
ENSRNOE00000286380
chr11:
24693851-24693771
81
A4_RAT
1-19
19
0
-
-
1.2
ENSRNOT00000048854
2
ENSRNOE00000014739
chr11:
24641638-24641471
168
A4_RAT
20-75
56
0
-
-
1.3
ENSRNOT00000048854
3
ENSRNOE00000014741
chr11:
24623995-24623866
130
A4_RAT
76-119
44
0
-
-
1.4
ENSRNOT00000048854
4
ENSRNOE00000014742
chr11:
24602576-24602464
113
A4_RAT
119-156
38
0
-
-
1.5
ENSRNOT00000048854
5
ENSRNOE00000014743
chr11:
24600007-24599814
194
A4_RAT
157-221
65
0
-
-
1.6
ENSRNOT00000048854
6
ENSRNOE00000294559
chr11:
24579923-24579721
203
A4_RAT
221-289
69
0
-
-
1.7b
ENSRNOT00000048854
7b
ENSRNOE00000014723
chr11:
24544293-24544126
168
A4_RAT
289-345
57
0
-
-
1.8
ENSRNOT00000048854
8
ENSRNOE00000014724
chr11:
24540940-24540884
57
A4_RAT
345-364
20
0
-
-
1.10a
ENSRNOT00000048854
10a
ENSRNOE00000365316
chr11:
24530072-24529939
134
A4_RAT
364-408
45
0
-
-
1.11
ENSRNOT00000048854
11
ENSRNOE00000014727
chr11:
24524460-24524386
75
A4_RAT
409-433
25
0
-
-
1.12
ENSRNOT00000048854
12
ENSRNOE00000323227
chr11:
24523995-24523837
159
A4_RAT
434-486
53
0
-
-
1.13
ENSRNOT00000048854
13
ENSRNOE00000014730
chr11:
24513499-24513371
129
A4_RAT
487-529
43
0
-
-
1.14
ENSRNOT00000048854
14
ENSRNOE00000341359
chr11:
24512019-24511920
100
A4_RAT
530-563
34
0
-
-
1.15
ENSRNOT00000048854
15
ENSRNOE00000014732
chr11:
24479343-24479122
222
A4_RAT
563-637
75
0
-
-
1.16
ENSRNOT00000048854
16
ENSRNOE00000014733
chr11:
24472983-24472930
54
A4_RAT
637-655
19
0
-
-
1.17
ENSRNOT00000048854
17
ENSRNOE00000014734
chr11:
24467388-24467288
101
A4_RAT
655-688
34
1
A:1-17
17
1.18
ENSRNOT00000048854
18
ENSRNOE00000347544
chr11:
24463735-24463589
147
A4_RAT
689-737
49
1
A:18-28
11
1.19a
ENSRNOT00000048854
19a
ENSRNOE00000349503
chr11:
24457959-24457855
105
A4_RAT
738-770
33
0
-
-
[
close EXON info
]
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1nmja_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Peptides
(792)
Fold
:
Amyloid peptides
(18)
Superfamily
:
Amyloid peptides
(18)
Family
:
Amyloid peptides
(18)
Protein domain
:
Alzheimer's disease amyloid beta-peptide
(15)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(1)
1a
d1nmja_
A:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Beta_APP_1nmjA01 (A:4-28)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Beta-APP]
(8)
Family
:
Beta-APP
(8)
Rattus norvegicus (Rat)
(1)
1a
Beta-APP-1nmjA01
A:4-28
[
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 (10 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
1NMJ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help