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.
3PQY
Asym. Unit
Info
Asym.Unit (535 KB)
Biol.Unit 1 (141 KB)
Biol.Unit 2 (139 KB)
Biol.Unit 3 (139 KB)
Biol.Unit 4 (138 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 6218 TCR IN COMPLEX WITH THE H2DB-PA224
Authors
:
S. Gras, C. Guillonneau, S. J. Turner, J. Rossjohn
Date
:
28 Nov 10 (Deposition) - 18 May 11 (Release) - 18 Jun 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.19
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P,Q,R,S,T
Biol. Unit 1: A,B,C,D,E (1x)
Biol. Unit 2: F,G,H,I,J (1x)
Biol. Unit 3: K,L,M,N,O (1x)
Biol. Unit 4: P,Q,R,S,T (1x)
Keywords
:
H2Db, Influenza, Tcr, T Cell, Pa Epitope, Repertoire, Viral Immunity, Chimeric Tcr, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
E. B. Day, C. Guillonneau, S. Gras, N. L. La Gruta, D. A. A. Vignali, P. C. Doherty, A. W. Purcell, J. Rossjohn, S. J. Turner
Structural Basis For Enabling T-Cell Receptor Diversity Within Biased Virus-Specific Cd8+ T-Cell Responses
Proc. Natl. Acad. Sci. Usa V. 108 9536 2011
[
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
(5, 20)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_B2MG_MOUSE_002 (H34Q, chain B/G/L/Q, )
2: VAR_B2MG_MOUSE_003 (K44E, chain B/G/L/Q, )
3: VAR_B2MG_MOUSE_004 (R81T, chain B/G/L/Q, )
4: VAR_B2MG_MOUSE_005 (D85D, chain B/G/L/Q, )
5: VAR_B2MG_MOUSE_006 (D85V, chain B/G/L/Q, )
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/G/L/Q
H
34
Q
2
UniProt
VAR_B2MG_MOUSE_003
*
K
64
E
B2MG_MOUSE
---
---
B/G/L/Q
K
44
E
3
UniProt
VAR_B2MG_MOUSE_004
*
R
101
T
B2MG_MOUSE
---
---
B/G/L/Q
R
81
T
4
UniProt
VAR_B2MG_MOUSE_005
*
A
105
D
B2MG_MOUSE
---
---
B/G/L/Q
D
85
D
5
UniProt
VAR_B2MG_MOUSE_006
*
A
105
V
B2MG_MOUSE
---
---
B/G/L/Q
D
85
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 8)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (B:78-84,G:78-84,L:78-84,Q:78-84,A:...)
;
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
4
B:78-84
G:78-84
L:78-84
Q:78-84
HA11_MOUSE
281-287
4
A:257-263
F:257-263
K:257-263
P:257-263
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_C1_set_3pqyQ01 (Q:11-92)
1b: PFAM_C1_set_3pqyQ02 (Q:11-92)
1c: PFAM_C1_set_3pqyQ03 (Q:11-92)
1d: PFAM_C1_set_3pqyQ04 (Q:11-92)
1e: PFAM_C1_set_3pqyP01 (P:189-271)
1f: PFAM_C1_set_3pqyP02 (P:189-271)
1g: PFAM_C1_set_3pqyP03 (P:189-271)
1h: PFAM_C1_set_3pqyP04 (P:189-271)
2a: PFAM_MHC_I_3pqyP05 (P:2-179)
2b: PFAM_MHC_I_3pqyP06 (P:2-179)
2c: PFAM_MHC_I_3pqyP07 (P:2-179)
2d: PFAM_MHC_I_3pqyP08 (P:2-179)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Mus musculus (Mouse)
(118)
1a
C1-set-3pqyQ01
Q:11-92
1b
C1-set-3pqyQ02
Q:11-92
1c
C1-set-3pqyQ03
Q:11-92
1d
C1-set-3pqyQ04
Q:11-92
1e
C1-set-3pqyP01
P:189-271
1f
C1-set-3pqyP02
P:189-271
1g
C1-set-3pqyP03
P:189-271
1h
C1-set-3pqyP04
P:189-271
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Mus musculus (Mouse)
(60)
2a
MHC_I-3pqyP05
P:2-179
2b
MHC_I-3pqyP06
P:2-179
2c
MHC_I-3pqyP07
P:2-179
2d
MHC_I-3pqyP08
P:2-179
[
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
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
Chain Q
Chain R
Chain S
Chain T
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 (535 KB)
Header - Asym.Unit
Biol.Unit 1 (141 KB)
Header - Biol.Unit 1
Biol.Unit 2 (139 KB)
Header - Biol.Unit 2
Biol.Unit 3 (139 KB)
Header - Biol.Unit 3
Biol.Unit 4 (138 KB)
Header - Biol.Unit 4
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
3PQY
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
