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...
Getting 'PROSITE' information from database.
PLEASE WAIT...
Getting 'Exon' information from database.
1LDR
Asym. Unit
Info
Asym.Unit (99 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
Models
(10 )
Title
:
SECOND REPEAT OF THE LDL RECEPTOR LIGAND-BINDING DOMAIN
Authors
:
N. L. Daly, J. T. Djordjevic, P. A. Kroon, R. Smith
Date
:
17 Aug 95 (Deposition) - 08 Mar 96 (Release) - 24 Feb 09 (Revision)
Method
:
SOLUTION NMR
Resolution
:
NOT APPLICABLE
Chains
:
Asym. Unit : A (10 x)
Keywords
:
Ldl Receptor Cysteine-Rich Repeat, Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
N. L. Daly, J. T. Djordjevic, P. A. Kroon, R. Smith
Three-Dimensional Structure Of The Second Cysteine-Rich Repeat From The Human Low-Density Lipoprotein Receptor.
Biochemistry V. 34 14474 1995
(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
(9, 9)
Info
(mutated residues are not available in "Model" view)
All SNPs/Variants
1: VAR_005307 (R15C, chain A, )
2: VAR_005308 (W24G, chain A, )
3: VAR_005309 (C26Y, chain A, )
4: VAR_005310 (D27G, chain A, )
5: VAR_005311 (D27N, chain A, )
6: VAR_005312 (D27Y, chain A, )
7: VAR_005313 (Q29E, chain A, )
8: VAR_005314 (C32G, chain A, )
9: VAR_005315 (E38K, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_005307
R
78
C
LDLR_HUMAN
Disease (FH)
---
A
R
15
C
2
UniProt
VAR_005308
W
87
G
LDLR_HUMAN
Disease (FH)
---
A
W
24
G
3
UniProt
VAR_005309
C
89
Y
LDLR_HUMAN
Disease (FH)
---
A
C
26
Y
4
UniProt
VAR_005310
D
90
G
LDLR_HUMAN
Disease (FH)
---
A
D
27
G
5
UniProt
VAR_005311
D
90
N
LDLR_HUMAN
Disease (FH)
---
A
D
27
N
6
UniProt
VAR_005312
D
90
Y
LDLR_HUMAN
Disease (FH)
---
A
D
27
Y
7
UniProt
VAR_005313
Q
92
E
LDLR_HUMAN
Disease (FH)
---
A
Q
29
E
8
UniProt
VAR_005314
C
95
G
LDLR_HUMAN
Disease (FH)
---
A
C
32
G
9
UniProt
VAR_005315
E
101
K
LDLR_HUMAN
Disease (FH)
---
A
E
38
K
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 2)
Info
All PROSITE Patterns/Profiles
1: LDLRA_2 (-|A:4-41|-|-|-|-|-)
2: LDLRA_1 (-|A:19-41|-|-|-|-|-)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
LDLRA_2
PS50068
LDL-receptor class A (LDLRA) domain profile.
LDLR_HUMAN
26-64
67-105
108-144
147-185
196-232
235-271
275-314
1
-
A:4-41
-
-
-
-
-
2
LDLRA_1
PS01209
LDL-receptor class A (LDLRA) domain signature.
LDLR_HUMAN
39-63
82-104
121-143
160-184
209-231
248-270
289-313
1
-
A:19-41
-
-
-
-
-
[
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.
SCOP Domains
(1, 1)
Info
All SCOP Domains
1a: SCOP_d1ldra_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Small proteins
(3458)
Fold
:
LDL receptor-like module
(20)
Superfamily
:
LDL receptor-like module
(20)
Family
:
LDL receptor-like module
(19)
Protein domain
:
Ligand-binding domain of low-density lipoprotein receptor
(13)
Human (Homo sapiens) [TaxId: 9606]
(13)
1a
d1ldra_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1ldrA00 (A:1-41)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Few Secondary Structures
(1120)
Architecture
:
Irregular
(1120)
Topology
:
Low-density Lipoprotein Receptor
(15)
Homologous Superfamily
:
Low-density Lipoprotein Receptor
(15)
Human (Homo sapiens)
(12)
1a
1ldrA00
A:1-41
[
close CATH info
]
Pfam Domains
(1, 1)
Info
all PFAM domains
1a: PFAM_Ldl_recept_a_1ldrA01 (A:3-41)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Ldl_recept_a]
(10)
Family
:
Ldl_recept_a
(10)
Homo sapiens (Human)
(9)
1a
Ldl_recept_a-1ldrA01
A:3-41
[
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 (99 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
1LDR
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help