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.
1ALY
Biol. Unit 1
Info
Asym.Unit (36 KB)
Biol.Unit 1 (92 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 HUMAN CD40 LIGAND
Authors
:
M. Karpusas, Y. M. Hsu, D. Thomas
Date
:
05 Jun 97 (Deposition) - 17 Sep 97 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.00
Chains
:
Asym. Unit : A
Biol. Unit 1: A (3x)
Keywords
:
Cd40L, Cd40 Ligand, Cytokine, Tnf, Hyper-Igm Syndrome
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Karpusas, Y. M. Hsu, J. H. Wang, J. Thompson, S. Lederman, L. Chess, D. Thomas
2 A Crystal Structure Of An Extracellular Fragment Of Human Cd40 Ligand.
Structure V. 3 1031 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
(31, 93)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
01: VAR_017929 (G116R, chain A, )
02: VAR_017930 (G116S, chain A, )
03: VAR_007514 (A123E, chain A, )
04: VAR_017926 (H125R, chain A, )
05: VAR_007515 (V126A, chain A, )
06: VAR_017931 (V126D, chain A, )
07: VAR_007517 (W140C, chain A, )
08: VAR_007518 (W140G, chain A, )
09: VAR_007519 (W140R, chain A, )
10: VAR_017932 (K143T, chain A, )
11: VAR_007520 (G144E, chain A, )
12: VAR_017922 (T147N, chain A, )
13: VAR_007521 (L155P, chain A, )
14: VAR_017923 (Y170C, chain A, )
15: VAR_017933 (A173D, chain A, )
16: VAR_017927 (Q174R, chain A, )
17: VAR_017934 (T176I, chain A, )
18: VAR_017935 (L195P, chain A, )
19: VAR_017936 (A208D, chain A, )
20: VAR_007522 (T211N, chain A, )
21: VAR_007523 (G219R, chain A, )
22: VAR_017937 (H224Y, chain A, )
23: VAR_017938 (G226A, chain A, )
24: VAR_007524 (G227V, chain A, )
25: VAR_007526 (L231S, chain A, )
26: VAR_007527 (A235P, chain A, )
27: VAR_017939 (V237E, chain A, )
28: VAR_007528 (T254M, chain A, )
29: VAR_017940 (G257D, chain A, )
30: VAR_017928 (G257S, chain A, )
31: VAR_017924 (L258S, chain A, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_017929
G
116
R
CD40L_HUMAN
Disease (HIGM1)
---
A
G
116
R
02
UniProt
VAR_017930
G
116
S
CD40L_HUMAN
Disease (HIGM1)
---
A
G
116
S
03
UniProt
VAR_007514
A
123
E
CD40L_HUMAN
Disease (HIGM1)
---
A
A
123
E
04
UniProt
VAR_017926
H
125
R
CD40L_HUMAN
Disease (HIGM1)
---
A
H
125
R
05
UniProt
VAR_007515
V
126
A
CD40L_HUMAN
Disease (HIGM1)
---
A
V
126
A
06
UniProt
VAR_017931
V
126
D
CD40L_HUMAN
Disease (HIGM1)
---
A
V
126
D
07
UniProt
VAR_007517
W
140
C
CD40L_HUMAN
Disease (HIGM1)
---
A
W
140
C
08
UniProt
VAR_007518
W
140
G
CD40L_HUMAN
Disease (HIGM1)
---
A
W
140
G
09
UniProt
VAR_007519
W
140
R
CD40L_HUMAN
Disease (HIGM1)
---
A
W
140
R
10
UniProt
VAR_017932
K
143
T
CD40L_HUMAN
Disease (HIGM1)
---
A
K
143
T
11
UniProt
VAR_007520
G
144
E
CD40L_HUMAN
Disease (HIGM1)
---
A
G
144
E
12
UniProt
VAR_017922
T
147
N
CD40L_HUMAN
Disease (HIGM1)
---
A
T
147
N
13
UniProt
VAR_007521
L
155
P
CD40L_HUMAN
Disease (HIGM1)
---
A
L
155
P
14
UniProt
VAR_017923
Y
170
C
CD40L_HUMAN
Disease (HIGM1)
---
A
Y
170
C
15
UniProt
VAR_017933
A
173
D
CD40L_HUMAN
Disease (HIGM1)
---
A
A
173
D
16
UniProt
VAR_017927
Q
174
R
CD40L_HUMAN
Disease (HIGM1)
---
A
Q
174
R
17
UniProt
VAR_017934
T
176
I
CD40L_HUMAN
Disease (HIGM1)
---
A
T
176
I
18
UniProt
VAR_017935
L
195
P
CD40L_HUMAN
Disease (HIGM1)
---
A
L
195
P
19
UniProt
VAR_017936
A
208
D
CD40L_HUMAN
Disease (HIGM1)
---
A
A
208
D
20
UniProt
VAR_007522
T
211
N
CD40L_HUMAN
Disease (HIGM1)
---
A
T
211
N
21
UniProt
VAR_007523
G
219
R
CD40L_HUMAN
Polymorphism
148594123
A
G
219
R
22
UniProt
VAR_017937
H
224
Y
CD40L_HUMAN
Disease (HIGM1)
---
A
H
224
Y
23
UniProt
VAR_017938
G
226
A
CD40L_HUMAN
Disease (HIGM1)
---
A
G
226
A
24
UniProt
VAR_007524
G
227
V
CD40L_HUMAN
Disease (HIGM1)
---
A
G
227
V
25
UniProt
VAR_007526
L
231
S
CD40L_HUMAN
Disease (HIGM1)
---
A
L
231
S
26
UniProt
VAR_007527
A
235
P
CD40L_HUMAN
Disease (HIGM1)
---
A
A
235
P
27
UniProt
VAR_017939
V
237
E
CD40L_HUMAN
Disease (HIGM1)
---
A
V
237
E
28
UniProt
VAR_007528
T
254
M
CD40L_HUMAN
Disease (HIGM1)
---
A
T
254
M
29
UniProt
VAR_017940
G
257
D
CD40L_HUMAN
Disease (HIGM1)
---
A
G
257
D
30
UniProt
VAR_017928
G
257
S
CD40L_HUMAN
Disease (HIGM1)
---
A
G
257
S
31
UniProt
VAR_017924
L
258
S
CD40L_HUMAN
Disease (HIGM1)
---
A
L
258
S
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(2, 6)
Info
All PROSITE Patterns/Profiles
1: TNF_2 (A:123-261)
2: TNF_1 (A:161-177)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
TNF_2
PS50049
TNF family profile.
CD40L_HUMAN
123-261
3
A:123-261
2
TNF_1
PS00251
TNF family signature.
CD40L_HUMAN
161-177
3
A:161-177
[
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, 1)
Info
All SCOP Domains
1a: SCOP_d1alya_ (A:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
TNF-like
(100)
Superfamily
:
TNF-like
(100)
Family
:
TNF-like
(82)
Protein domain
:
Extracellular domain of CD40 ligand
(2)
Human (Homo sapiens) [TaxId: 9606]
(2)
1a
d1alya_
A:
[
close SCOP info
]
CATH Domains
(1, 1)
Info
all CATH domains
1a: CATH_1alyA00 (A:116-261)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Jelly Rolls
(1293)
Homologous Superfamily
:
[code=2.60.120.40, no name defined]
(56)
Human (Homo sapiens)
(38)
1a
1alyA00
A:116-261
[
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
Asymmetric Unit 1
Asymmetric Unit 2
Asymmetric Unit 3
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 (36 KB)
Header - Asym.Unit
Biol.Unit 1 (92 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
1ALY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help