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.
3RTQ
Asym. Unit
Info
Asym.Unit (285 KB)
Biol.Unit 1 (278 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-HS44-INKT TCR COMPLEX
Authors
:
E. D. Yu, D. M. Zajonc
Date
:
03 May 11 (Deposition) - 22 Feb 12 (Release) - 18 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B,C,D (1x)
Keywords
:
Antigen Presentation, Glycolipid, Nkt Cells, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
J. Kerzerho, E. D. Yu, C. M. Barra, E. Alari-Pahisa, E. Girardi, Y. Harrak, P. Lauzurica, A. Llebaria, D. M. Zajonc, O. Akbari, A. R. Castano
Structural And Functional Characterization Of A Novel Nonglycosidic Type I Nkt Agonist With Immunomodulatory Properties.
J. Immunol. V. 188 2254 2012
[
close entry info
]
Hetero Components
(4, 8)
Info
All Hetero Components
1a: BETA-D-MANNOSE (BMAa)
2a: BETA-L-FUCOSE (FULa)
3a: N-[(2S,3S,4R)-3,4-DIHYDROXY-1-{[(1... (H4Sa)
4a: N-ACETYL-D-GLUCOSAMINE (NAGa)
4b: N-ACETYL-D-GLUCOSAMINE (NAGb)
4c: N-ACETYL-D-GLUCOSAMINE (NAGc)
4d: N-ACETYL-D-GLUCOSAMINE (NAGd)
4e: N-ACETYL-D-GLUCOSAMINE (NAGe)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
BMA
1
Ligand/Ion
BETA-D-MANNOSE
2
FUL
1
Ligand/Ion
BETA-L-FUCOSE
3
H4S
1
Ligand/Ion
N-[(2S,3S,4R)-3,4-DIHYDROXY-1-{[(1S,2S,3R,4R,5S)-2,3,4,5-TETRAHYDROXYCYCLOHEXYL]AMINO}OCTADECAN-2-YL]HEXACOSANAMIDE
4
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: AC7 (SOFTWARE)
8: AC8 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ALA A:19 , ASN A:20 , TRP A:23
BINDING SITE FOR RESIDUE NAG A 286
2
AC2
SOFTWARE
TRP A:23 , SER A:24 , ASN A:42 , NAG A:288
BINDING SITE FOR RESIDUE NAG A 287
3
AC3
SOFTWARE
NAG A:287
BINDING SITE FOR RESIDUE NAG A 288
4
AC4
SOFTWARE
GLY A:130 , GLN A:161 , ASN A:165 , NAG A:290 , FUL A:292
BINDING SITE FOR RESIDUE NAG A 289
5
AC5
SOFTWARE
GLY A:130 , NAG A:289 , BMA A:291
BINDING SITE FOR RESIDUE NAG A 290
6
AC6
SOFTWARE
NAG A:290
BINDING SITE FOR RESIDUE BMA A 291
7
AC7
SOFTWARE
SER A:114 , PHE A:128 , TRP A:129 , GLY A:130 , LEU A:164 , NAG A:289
BINDING SITE FOR RESIDUE FUL A 292
8
AC8
SOFTWARE
SER A:28 , PHE A:70 , TYR A:73 , ASP A:80 , TRP A:133 , LEU A:150 , ASP A:153 , GLY A:155 , THR A:156 , PHE A:171 , HOH A:294 , PRO C:28 , ASN C:30 , ARG C:95 , GLY C:96
BINDING SITE FOR RESIDUE H4S A 293
[
close Site info
]
SAPs(SNPs)/Variants
(5, 5)
Info
(mutated residues are not available)
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.
SCOP Domains
(6, 7)
Info
All SCOP Domains
1a: SCOP_d3rtqc1 (C:1-117)
1b: SCOP_d3rtqd2 (D:113-240)
2a: SCOP_d3rtqa2 (A:186-279)
3a: SCOP_d3rtqb_ (B:)
4a: SCOP_d3rtqc2 (C:118-206)
5a: SCOP_d3rtqd1 (D:2-112)
6a: SCOP_d3rtqa1 (A: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
d3rtqc1
C:1-117
1b
d3rtqd2
D:113-240
Family
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
2a
d3rtqa2
A:186-279
Protein domain
:
beta2-microglobulin
(530)
Mouse (Mus musculus) [TaxId: 10090]
(166)
3a
d3rtqb_
B:
Protein domain
:
T-cell antigen receptor
(81)
Mouse (Mus musculus) [TaxId: 10090]
(2)
4a
d3rtqc2
C:118-206
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
T-cell antigen receptor
(105)
Mouse (Mus musculus), beta-chain [TaxId: 10090]
(28)
5a
d3rtqd1
D:2-112
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)
6a
d3rtqa1
A: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 (285 KB)
Header - Asym.Unit
Biol.Unit 1 (278 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
3RTQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
