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.
1EDY
Asym. Unit
Info
Asym.Unit (49 KB)
Biol.Unit 1 (91 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 RAT ALPHA 1-MACROGLOBULIN RECEPTOR BINDING DOMAIN
Authors
:
T. Xiao, D. L. Decamp, S. R. Sprang
Date
:
28 Jan 00 (Deposition) - 01 Dec 00 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (2x)
Keywords
:
Beta Sandwich, Pseudo-Symmetric Dimer, Protein Binding
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Xiao, D. L. Decamp, S. R. Spran
Structure Of A Rat Alpha 1-Macroglobulin Receptor-Binding Domain Dimer.
Protein Sci. V. 9 1889 2000
(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
(6, 11)
Info
All Exons
Exon 1.31 (A:3-33 | B:3-33)
Exon 1.32 (A:33-63 | B:33-63)
Exon 1.33 (A:64-86 | B:64-86)
Exon 1.34 (A:87-121 | B:87-121)
Exon 1.35 (A:121-135 | B:121-132)
Exon 1.36 (A:135-136 | -)
View:
Select:
Label:
All Exon Boundaries
1: Boundary 1.30/1.31
2: Boundary 1.31/1.32
3: Boundary 1.32/1.33
4: Boundary 1.33/1.34
5: Boundary 1.34/1.35
6: Boundary 1.35/1.36
7: Boundary 1.36/-
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
ENSRNOT00000009467
1
ENSRNOE00000061288
chr4:
165551145-165551009
137
A1M_RAT
1-29
29
0
-
-
1.2
ENSRNOT00000009467
2
ENSRNOE00000061503
chr4:
165549994-165549811
184
A1M_RAT
29-90
62
0
-
-
1.3
ENSRNOT00000009467
3
ENSRNOE00000061664
chr4:
165548811-165548658
154
A1M_RAT
91-142
52
0
-
-
1.4
ENSRNOT00000009467
4
ENSRNOE00000376989
chr4:
165548470-165548418
53
A1M_RAT
142-159
18
0
-
-
1.5
ENSRNOT00000009467
5
ENSRNOE00000376985
chr4:
165547431-165547411
21
A1M_RAT
160-166
7
0
-
-
1.6
ENSRNOT00000009467
6
ENSRNOE00000061988
chr4:
165546883-165546715
169
A1M_RAT
167-223
57
0
-
-
1.7
ENSRNOT00000009467
7
ENSRNOE00000062151
chr4:
165545886-165545802
85
A1M_RAT
223-251
29
0
-
-
1.8
ENSRNOT00000009467
8
ENSRNOE00000062308
chr4:
165542552-165542429
124
A1M_RAT
251-292
42
0
-
-
1.9
ENSRNOT00000009467
9
ENSRNOE00000062465
chr4:
165539632-165539518
115
A1M_RAT
293-331
39
0
-
-
1.10
ENSRNOT00000009467
10
ENSRNOE00000062620
chr4:
165538978-165538869
110
A1M_RAT
331-367
37
0
-
-
1.11
ENSRNOT00000009467
11
ENSRNOE00000062790
chr4:
165536648-165536487
162
A1M_RAT
368-421
54
0
-
-
1.12
ENSRNOT00000009467
12
ENSRNOE00000062948
chr4:
165535737-165535510
228
A1M_RAT
422-497
76
0
-
-
1.13
ENSRNOT00000009467
13
ENSRNOE00000063097
chr4:
165534524-165534461
64
A1M_RAT
498-519
22
0
-
-
1.14
ENSRNOT00000009467
14
ENSRNOE00000063254
chr4:
165527893-165527751
143
A1M_RAT
519-566
48
0
-
-
1.15
ENSRNOT00000009467
15
ENSRNOE00000063406
chr4:
165525360-165525211
150
A1M_RAT
567-616
50
0
-
-
1.16
ENSRNOT00000009467
16
ENSRNOE00000063572
chr4:
165523870-165523706
165
A1M_RAT
617-671
55
0
-
-
1.17
ENSRNOT00000009467
17
ENSRNOE00000063747
chr4:
165521191-165521098
94
A1M_RAT
672-703
32
0
-
-
1.18
ENSRNOT00000009467
18
ENSRNOE00000063897
chr4:
165519302-165519128
175
A1M_RAT
703-761
59
0
-
-
1.19
ENSRNOT00000009467
19
ENSRNOE00000064021
chr4:
165518734-165518506
229
A1M_RAT
761-837
77
0
-
-
1.20
ENSRNOT00000009467
20
ENSRNOE00000064193
chr4:
165517914-165517788
127
A1M_RAT
838-880
43
0
-
-
1.21
ENSRNOT00000009467
21
ENSRNOE00000064356
chr4:
165517405-165517284
122
A1M_RAT
880-920
41
0
-
-
1.22
ENSRNOT00000009467
22
ENSRNOE00000064527
chr4:
165517079-165517028
52
A1M_RAT
921-938
18
0
-
-
1.23
ENSRNOT00000009467
23
ENSRNOE00000064695
chr4:
165513810-165513727
84
A1M_RAT
938-966
29
0
-
-
1.24
ENSRNOT00000009467
24
ENSRNOE00000064862
chr4:
165513268-165513092
177
A1M_RAT
966-1025
60
0
-
-
1.25
ENSRNOT00000009467
25
ENSRNOE00000065032
chr4:
165512822-165512732
91
A1M_RAT
1025-1055
31
0
-
-
1.26
ENSRNOT00000009467
26
ENSRNOE00000350117
chr4:
165512261-165512105
157
A1M_RAT
1055-1107
53
0
-
-
1.27
ENSRNOT00000009467
27
ENSRNOE00000344825
chr4:
165511699-165511625
75
A1M_RAT
1108-1132
25
0
-
-
1.28
ENSRNOT00000009467
28
ENSRNOE00000065559
chr4:
165511349-165511172
178
A1M_RAT
1133-1192
60
0
-
-
1.29
ENSRNOT00000009467
29
ENSRNOE00000065720
chr4:
165510481-165510231
251
A1M_RAT
1192-1275
84
0
-
-
1.30
ENSRNOT00000009467
30
ENSRNOE00000065855
chr4:
165509498-165509280
219
A1M_RAT
1276-1348
73
0
-
-
1.31
ENSRNOT00000009467
31
ENSRNOE00000066003
chr4:
165509107-165508977
131
A1M_RAT
1349-1392
44
2
A:3-33
B:3-33
31
31
1.32
ENSRNOT00000009467
32
ENSRNOE00000066146
chr4:
165508590-165508500
91
A1M_RAT
1392-1422
31
2
A:33-63
B:33-63
31
31
1.33
ENSRNOT00000009467
33
ENSRNOE00000066311
chr4:
165507986-165507918
69
A1M_RAT
1423-1445
23
2
A:64-86
B:64-86
23
23
1.34
ENSRNOT00000009467
34
ENSRNOE00000066471
chr4:
165506877-165506775
103
A1M_RAT
1446-1480
35
2
A:87-121
B:87-121
35
35
1.35
ENSRNOT00000009467
35
ENSRNOE00000066623
chr4:
165505970-165505929
42
A1M_RAT
1480-1494
15
2
A:121-135
B:121-132
15
12
1.36
ENSRNOT00000009467
36
ENSRNOE00000332012
chr4:
165505230-165505085
146
A1M_RAT
1494-1500
7
1
A:135-136
-
2
-
[
close EXON info
]
SCOP Domains
(1, 2)
Info
All SCOP Domains
1a: SCOP_d1edya_ (A:)
1b: SCOP_d1edyb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Macroglobulin
(20)
Family
:
Alpha-macroglobulin receptor domain
(5)
Protein domain
:
alpha-1-macroglobulin
(1)
Norway rat (Rattus norvegicus) [TaxId: 10116]
(1)
1a
d1edya_
A:
1b
d1edyb_
B:
[
close SCOP info
]
CATH Domains
(1, 2)
Info
all CATH domains
1a: CATH_1edyA00 (A:3-136)
1b: CATH_1edyB00 (B:3-132)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
[code=2.60.40.690, no name defined]
(3)
Norway rat (Rattus norvegicus)
(1)
1a
1edyA00
A:3-136
1b
1edyB00
B:3-132
[
close CATH info
]
Pfam Domains
(0, 0)
Info
all PFAM domains
View:
Select:
Label:
Sorry, no Info available
[
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
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 (49 KB)
Header - Asym.Unit
Biol.Unit 1 (91 KB)
Header - Biol.Unit 1
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
1EDY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
