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.
1N3N
Biol. Unit 6
Info
Asym.Unit (247 KB)
Biol.Unit 1 (64 KB)
Biol.Unit 2 (64 KB)
Biol.Unit 3 (64 KB)
Biol.Unit 4 (64 KB)
Biol.Unit 5 (122 KB)
Biol.Unit 6 (124 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 A MYCOBACTERIAL HSP60 EPITOPE WITH THE MURINE CLASS I MHC MOLECULE H-2DB
Authors
:
C. Ciatto, G. Capitani, A. C. Tissot, F. Pecorari, A. Pluckthun, M. G. Grutter
Date
:
29 Oct 02 (Deposition) - 27 May 03 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L
Biol. Unit 1: A,B,I (1x)
Biol. Unit 2: G,H,L (1x)
Biol. Unit 3: E,F,K (1x)
Biol. Unit 4: C,D,J (1x)
Biol. Unit 5: C,D,G,H,J,L (1x)
Biol. Unit 6: A,B,E,F,I,K (1x)
Keywords
:
Immunoglobulin Fold, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
C. Ciatto, G. Capitani, A. C. Tissot, F. Pecorari, A. Plueckthun, M. G. Gruetter
Structural Analysis Of Mycobacterial And Murine Hsp60 Epitopes In Complex With The Class I Mhc Molecule H-2D(B)
Febs Lett. V. 543 11 2003
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 1)
Info
All Hetero Components
1a: SULFATE ION (SO4a)
1b: SULFATE ION (SO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SO4
1
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(1, 1)
Info
All Sites
1: AC1 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG E:14 , PRO E:15 , GLY E:16 , LEU E:17 , GLY E:90 , GLY E:91
BINDING SITE FOR RESIDUE SO4 E 281
[
close Site info
]
SAPs(SNPs)/Variants
(5, 10)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
1: VAR_B2MG_MOUSE_002 (H34Q, chain B/F, )
2: VAR_B2MG_MOUSE_003 (K44E, chain B/F, )
3: VAR_B2MG_MOUSE_004 (R81T, chain B/F, )
4: VAR_B2MG_MOUSE_005 (D85D, chain B/F, )
5: VAR_B2MG_MOUSE_006 (D85V, chain B/F, )
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/F
H
34
Q
2
UniProt
VAR_B2MG_MOUSE_003
*
K
64
E
B2MG_MOUSE
---
---
B/F
K
44
E
3
UniProt
VAR_B2MG_MOUSE_004
*
R
101
T
B2MG_MOUSE
---
---
B/F
R
81
T
4
UniProt
VAR_B2MG_MOUSE_005
*
A
105
D
B2MG_MOUSE
---
---
B/F
D
85
D
5
UniProt
VAR_B2MG_MOUSE_006
*
A
105
V
B2MG_MOUSE
---
---
B/F
D
85
V
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 4)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (A:257-263,E: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
2
B:78-84
-
F:78-84
-
HA11_MOUSE
281-287
2
A:257-263
-
E: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
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1n3nb_ (B:)
1b: SCOP_d1n3nd_ (D:)
1c: SCOP_d1n3nf_ (F:)
1d: SCOP_d1n3nh_ (H:)
2a: SCOP_d1n3na1 (A:182-276)
2b: SCOP_d1n3nc1 (C:182-276)
2c: SCOP_d1n3ne1 (E:182-276)
2d: SCOP_d1n3ng1 (G:182-276)
3a: SCOP_d1n3na2 (A:1-181)
3b: SCOP_d1n3nc2 (C:1-181)
3c: SCOP_d1n3ne2 (E:1-181)
3d: SCOP_d1n3ng2 (G: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
d1n3nb_
B:
1b
d1n3nd_
D:
1c
d1n3nf_
F:
1d
d1n3nh_
H:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Mouse (Mus musculus) [TaxId: 10090]
(102)
2a
d1n3na1
A:182-276
2b
d1n3nc1
C:182-276
2c
d1n3ne1
E:182-276
2d
d1n3ng1
G:182-276
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-2DB [TaxId: 10090]
(25)
3a
d1n3na2
A:1-181
3b
d1n3nc2
C:1-181
3c
d1n3ne2
E:1-181
3d
d1n3ng2
G:1-181
[
close SCOP info
]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1n3nA01 (A:1-181)
1b: CATH_1n3nC01 (C:1-181)
1c: CATH_1n3nE01 (E:1-181)
1d: CATH_1n3nG01 (G:1-181)
2a: CATH_1n3nB00 (B:1-99)
2b: CATH_1n3nA02 (A:182-272)
2c: CATH_1n3nC02 (C:182-272)
2d: CATH_1n3nE02 (E:182-272)
2e: CATH_1n3nG02 (G:182-272)
2f: CATH_1n3nD00 (D:1-99)
2g: CATH_1n3nF00 (F:1-99)
2h: CATH_1n3nH00 (H:1-99)
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
1n3nA01
A:1-181
1b
1n3nC01
C:1-181
1c
1n3nE01
E:1-181
1d
1n3nG01
G:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
House mouse (Mus musculus)
(616)
2a
1n3nB00
B:1-99
2b
1n3nA02
A:182-272
2c
1n3nC02
C:182-272
2d
1n3nE02
E:182-272
2e
1n3nG02
G:182-272
2f
1n3nD00
D:1-99
2g
1n3nF00
F:1-99
2h
1n3nH00
H:1-99
[
close CATH info
]
Pfam Domains
(2, 12)
Info
all PFAM domains
1a: PFAM_C1_set_1n3nH01 (H:11-92)
1b: PFAM_C1_set_1n3nH02 (H:11-92)
1c: PFAM_C1_set_1n3nH03 (H:11-92)
1d: PFAM_C1_set_1n3nH04 (H:11-92)
1e: PFAM_C1_set_1n3nG01 (G:189-271)
1f: PFAM_C1_set_1n3nG02 (G:189-271)
1g: PFAM_C1_set_1n3nG03 (G:189-271)
1h: PFAM_C1_set_1n3nG04 (G:189-271)
2a: PFAM_MHC_I_1n3nG05 (G:1-179)
2b: PFAM_MHC_I_1n3nG06 (G:1-179)
2c: PFAM_MHC_I_1n3nG07 (G:1-179)
2d: PFAM_MHC_I_1n3nG08 (G:1-179)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
Ig
(577)
Family
:
C1-set
(338)
Mus musculus (Mouse)
(118)
1a
C1-set-1n3nH01
H:11-92
1b
C1-set-1n3nH02
H:11-92
1c
C1-set-1n3nH03
H:11-92
1d
C1-set-1n3nH04
H:11-92
1e
C1-set-1n3nG01
G:189-271
1f
C1-set-1n3nG02
G:189-271
1g
C1-set-1n3nG03
G:189-271
1h
C1-set-1n3nG04
G:189-271
Clan
:
MHC
(252)
Family
:
MHC_I
(210)
Mus musculus (Mouse)
(60)
2a
MHC_I-1n3nG05
G:1-179
2b
MHC_I-1n3nG06
G:1-179
2c
MHC_I-1n3nG07
G:1-179
2d
MHC_I-1n3nG08
G:1-179
[
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 E
Chain F
Chain I
Chain K
Asymmetric Unit 1
Asymmetric Unit 2
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 (247 KB)
Header - Asym.Unit
Biol.Unit 1 (64 KB)
Header - Biol.Unit 1
Biol.Unit 2 (64 KB)
Header - Biol.Unit 2
Biol.Unit 3 (64 KB)
Header - Biol.Unit 3
Biol.Unit 4 (64 KB)
Header - Biol.Unit 4
Biol.Unit 5 (122 KB)
Header - Biol.Unit 5
Biol.Unit 6 (124 KB)
Header - Biol.Unit 6
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
1N3N
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help