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.
3TVM
Biol. Unit 1
Info
Asym.Unit (530 KB)
Biol.Unit 1 (273 KB)
Biol.Unit 2 (253 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
STRUCTURE OF THE MOUSE CD1D-SMC124-INKT TCR COMPLEX
Authors
:
E. Girardi, Y. Li, D. M. Zajonc
Date
:
20 Sep 11 (Deposition) - 01 Feb 12 (Release) - 01 Feb 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Keywords
:
Antigen Presentation, Glycolipid, Nkt Cells, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. J. Tyznik, E. Farber, E. Girardi, A. Birkholz, Y. Li, S. Chitale, R. So, P. Arora, A. Khurana, J. Wang, S. A. Porcelli, D. M. Zajonc, M. Kronenberg, A. R. Howell
Glycolipids That Elicit Ifn-Gama-Biased Responses From Natural Killer T Cells
Chem. Biol. V. 18 1620 2011
[
close entry info
]
Hetero Components
(3, 7)
Info
All Hetero Components
1a: N-[(2S,3R)-10-[(1R,2R)-2-DECYLCYCL... (07Pa)
1b: N-[(2S,3R)-10-[(1R,2R)-2-DECYLCYCL... (07Pb)
2a: CHLORIDE ION (CLa)
3a: ALPHA-L-FUCOSE (FUCa)
3b: ALPHA-L-FUCOSE (FUCb)
4a: GLYCEROL (GOLa)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
5d: N-ACETYL-D-GLUCOSAMINE (NAGd)
5e: N-ACETYL-D-GLUCOSAMINE (NAGe)
5f: N-ACETYL-D-GLUCOSAMINE (NAGf)
5g: N-ACETYL-D-GLUCOSAMINE (NAGg)
5h: N-ACETYL-D-GLUCOSAMINE (NAGh)
5i: N-ACETYL-D-GLUCOSAMINE (NAGi)
5j: N-ACETYL-D-GLUCOSAMINE (NAGj)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
07P
1
Ligand/Ion
N-[(2S,3R)-10-[(1R,2R)-2-DECYLCYCLOPROPYL]-1-(ALPHA-D-GALACTOPYRANOSYLOXY)-3-HYDROXYDECAN-2-YL]HEXACOSANAMIDE
2
CL
-1
Ligand/Ion
CHLORIDE ION
3
FUC
1
Ligand/Ion
ALPHA-L-FUCOSE
4
GOL
-1
Ligand/Ion
GLYCEROL
5
NAG
5
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
[
close Hetero Component info
]
Sites
(8, 8)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: BC4 (SOFTWARE)
8: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:19 , ASN A:20 , SER A:22
BINDING SITE FOR RESIDUE NAG A 508
2
AC2
SOFTWARE
TRP A:23 , SER A:24 , ASN A:42 , NAG A:510
BINDING SITE FOR RESIDUE NAG A 509
3
AC3
SOFTWARE
NAG A:509
BINDING SITE FOR RESIDUE NAG A 510
4
AC4
SOFTWARE
GLY A:130 , GLN A:161 , ASN A:165 , NAG A:512 , FUC A:513
BINDING SITE FOR RESIDUE NAG A 511
5
AC5
SOFTWARE
GLY A:130 , NAG A:511
BINDING SITE FOR RESIDUE NAG A 512
6
AC6
SOFTWARE
SER A:114 , GLY A:130 , ASN A:165 , NAG A:511
BINDING SITE FOR RESIDUE FUC A 513
7
BC4
SOFTWARE
SER A:28 , VAL A:30 , TRP A:63 , TYR A:73 , SER A:76 , ASP A:80 , VAL A:118 , TRP A:133 , LEU A:143 , ASP A:153 , GLY A:155 , THR A:156 , THR A:159 , CYS A:168 , PHE A:171 , PRO C:28 , ASN C:30 , ARG C:95 , GLY C:96
BINDING SITE FOR RESIDUE 07P A 286
8
BC6
SOFTWARE
HIS D:164 , SER D:165
BINDING SITE FOR RESIDUE CL D 241
[
close Site info
]
SAPs(SNPs)/Variants
(5, 5)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_B2MG_MOUSE_002 (H34Q, chain B, )
2: VAR_B2MG_MOUSE_003 (K44E, chain B, )
3: VAR_B2MG_MOUSE_004 (R81T, chain B, )
4: VAR_B2MG_MOUSE_005 (A85D, chain B, )
5: VAR_B2MG_MOUSE_006 (A85V, chain B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_B2MG_MOUSE_002
*
H
54
Q
B2MG_MOUSE
---
---
B
H
34
Q
2
UniProt
VAR_B2MG_MOUSE_003
*
K
64
E
B2MG_MOUSE
---
---
B
K
44
E
3
UniProt
VAR_B2MG_MOUSE_004
*
R
101
T
B2MG_MOUSE
---
---
B
R
81
T
4
UniProt
VAR_B2MG_MOUSE_005
*
A
105
D
B2MG_MOUSE
---
---
B
A
85
D
5
UniProt
VAR_B2MG_MOUSE_006
*
A
105
V
B2MG_MOUSE
---
---
B
A
85
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:78-84)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
IG_MHC
PS00290
Immunoglobulins and major histocompatibility complex proteins signature.
B2MG_MOUSE
98-104
1
B:78-84
-
[
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
(5, 14)
Info
All SCOP Domains
1a: SCOP_d3tvmc1 (C:1-117)
1b: SCOP_d3tvmg1 (G:1-117)
2a: SCOP_d3tvma2 (A:186-279)
2b: SCOP_d3tvmc2 (C:118-206)
2c: SCOP_d3tvmd2 (D:113-240)
2d: SCOP_d3tvme2 (E:186-249)
2e: SCOP_d3tvmg2 (G:118-206)
2f: SCOP_d3tvmh2 (H:113-240)
3a: SCOP_d3tvmb_ (B:)
3b: SCOP_d3tvmf_ (F:)
4a: SCOP_d3tvmd1 (D:2-112)
4b: SCOP_d3tvmh1 (H:1-112)
5a: SCOP_d3tvma1 (A:6-185)
5b: SCOP_d3tvme1 (E:7-185)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
Immunoglobulin-like beta-sandwich
(7299)
Superfamily
:
Immunoglobulin
(5995)
Family
:
automated matches
(864)
Protein domain
:
automated matches
(864)
Mouse (Mus musculus) [TaxId: 10090]
(360)
1a
d3tvmc1
C:1-117
1b
d3tvmg1
G:1-117
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
2a
d3tvma2
A:186-279
2b
d3tvmc2
C:118-206
2c
d3tvmd2
D:113-240
2d
d3tvme2
E:186-249
2e
d3tvmg2
G:118-206
2f
d3tvmh2
H:113-240
Protein domain
:
beta2-microglobulin
(530)
Mouse (Mus musculus) [TaxId: 10090]
(166)
3a
d3tvmb_
B:
3b
d3tvmf_
F:
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
automated matches
(311)
Mouse (Mus musculus) [TaxId: 10090]
(112)
4a
d3tvmd1
D:2-112
4b
d3tvmh1
H:1-112
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
automated matches
(52)
Protein domain
:
automated matches
(52)
Mouse (Mus musculus) [TaxId: 10090]
(29)
5a
d3tvma1
A:6-185
5b
d3tvme1
E:7-185
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
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
Chain C
Chain D
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 (530 KB)
Header - Asym.Unit
Biol.Unit 1 (273 KB)
Header - Biol.Unit 1
Biol.Unit 2 (253 KB)
Header - Biol.Unit 2
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
3TVM
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
