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.
1BQH
Biol. Unit 1
Info
Asym.Unit (214 KB)
Biol.Unit 1 (106 KB)
Biol.Unit 2 (106 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MURINE CD8AA ECTODOMAIN FRAGMENT IN COMPLEX WITH H-2KB/VSV8
Authors
:
J. H. Wang, E. L. Reinherz, P. S. Kern, H. C. Chang
Date
:
16 Aug 98 (Deposition) - 19 Aug 98 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.80
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,K
Biol. Unit 1: A,B,C,G,H (1x)
Biol. Unit 2: D,E,F,I,K (1x)
Keywords
:
T-Cell, Coreceptor, Glycoprotein, Complex, Immunology, Antigen, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. S. Kern, M. K. Teng, A. Smolyar, J. H. Liu, J. Liu, R. E. Hussey, R. Spoerl, H. C. Chang, E. L. Reinherz, J. H. Wang
Structural Basis Of Cd8 Coreceptor Function Revealed By Crystallographic Analysis Of A Murine Cd8Alphaalpha Ectodomain Fragment In Complex With H-2Kb.
Immunity V. 9 519 1998
[
close entry info
]
Hetero Components
(2, 2)
Info
All Hetero Components
1a: N-ACETYL-D-GLUCOSAMINE (NAGa)
1b: N-ACETYL-D-GLUCOSAMINE (NAGb)
1c: N-ACETYL-D-GLUCOSAMINE (NAGc)
2a: 2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOP... (NDGa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
NAG
1
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
2
NDG
1
Ligand/Ion
2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE
[
close Hetero Component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
PHE G:40 , ASN G:42 , SER G:43 , LYS G:94 , GLU G:95
BINDING SITE FOR RESIDUE NDG G 130
2
AC2
SOFTWARE
PHE H:40 , ASN H:42 , SER H:44 , GLU H:95
BINDING SITE FOR RESIDUE NAG H 130
[
close Site info
]
SAPs(SNPs)/Variants
(6, 7)
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_CD8A_MOUSE_001 (M78V, chain G/H, )
4: VAR_B2MG_MOUSE_004 (R81T, chain B, )
5: VAR_B2MG_MOUSE_005 (D85D, chain B, )
6: VAR_B2MG_MOUSE_006 (D85V, 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_CD8A_MOUSE_001
*
M
105
V
CD8A_MOUSE
---
---
G/H
M
78
V
4
UniProt
VAR_B2MG_MOUSE_004
*
R
101
T
B2MG_MOUSE
---
---
B
R
81
T
5
UniProt
VAR_B2MG_MOUSE_005
*
A
105
D
B2MG_MOUSE
---
---
B
D
85
D
6
UniProt
VAR_B2MG_MOUSE_006
*
A
105
V
B2MG_MOUSE
---
---
B
D
85
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 2)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (A:257-263)
;
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
-
HA1B_MOUSE
278-284
1
A: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.
(no "Exon" information available for biological units yet)
SCOP Domains
(4, 10)
Info
All SCOP Domains
1a: SCOP_d1bqhb_ (B:)
1b: SCOP_d1bqhe_ (E:)
2a: SCOP_d1bqha1 (A:182-274)
2b: SCOP_d1bqhd1 (D:182-274)
3a: SCOP_d1bqhg_ (G:)
3b: SCOP_d1bqhh_ (H:)
3c: SCOP_d1bqhi_ (I:)
3d: SCOP_d1bqhk_ (K:)
4a: SCOP_d1bqha2 (A:1-181)
4b: SCOP_d1bqhd2 (D:1-181)
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
:
C1 set domains (antibody constant domain-like)
(3013)
Protein domain
:
beta2-microglobulin
(530)
Mouse (Mus musculus) [TaxId: 10090]
(166)
1a
d1bqhb_
B:
1b
d1bqhe_
E:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Mouse (Mus musculus) [TaxId: 10090]
(102)
2a
d1bqha1
A:182-274
2b
d1bqhd1
D:182-274
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
CD8
(10)
Mouse (Mus musculus) [TaxId: 10090]
(5)
3a
d1bqhg_
G:
3b
d1bqhh_
H:
3c
d1bqhi_
I:
3d
d1bqhk_
K:
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
MHC antigen-recognition domain
(585)
Superfamily
:
MHC antigen-recognition domain
(585)
Family
:
MHC antigen-recognition domain
(533)
Protein domain
:
Class I MHC, alpha-1 and alpha-2 domains
(294)
Mouse (Mus musculus), H-2KB [TaxId: 10090]
(42)
4a
d1bqha2
A:1-181
4b
d1bqhd2
D:1-181
[
close SCOP info
]
CATH Domains
(2, 10)
Info
all CATH domains
1a: CATH_1bqhA01 (A:1-181)
1b: CATH_1bqhD01 (D:1-181)
2a: CATH_1bqhB00 (B:1-99)
2b: CATH_1bqhA02 (A:182-272)
2c: CATH_1bqhD02 (D:182-272)
2d: CATH_1bqhE00 (E:1-99)
2e: CATH_1bqhG00 (G:1-122)
2f: CATH_1bqhI00 (I:4-125)
2g: CATH_1bqhH00 (H:1-125)
2h: CATH_1bqhK00 (K:1-125)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
Murine Class I Major Histocompatibility Complex, H2-DB; Chain A, domain 1
(402)
Homologous Superfamily
:
Murine Class I Major Histocompatibility Complex, H2-DB, subunit A, domain 1
(400)
House mouse (Mus musculus)
(92)
1a
1bqhA01
A:1-181
1b
1bqhD01
D:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
House mouse (Mus musculus)
(616)
2a
1bqhB00
B:1-99
2b
1bqhA02
A:182-272
2c
1bqhD02
D:182-272
2d
1bqhE00
E:1-99
2e
1bqhG00
G:1-122
2f
1bqhI00
I:4-125
2g
1bqhH00
H:1-125
2h
1bqhK00
K:1-125
[
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 G
Chain H
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 (214 KB)
Header - Asym.Unit
Biol.Unit 1 (106 KB)
Header - Biol.Unit 1
Biol.Unit 2 (106 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
1BQH
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
