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.
1FZM
Asym. Unit
Info
Asym.Unit (78 KB)
Biol.Unit 1 (73 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
MHC CLASS I NATURAL MUTANT H-2KBM8 HEAVY CHAIN COMPLEXED WITH BETA-2 MICROGLOBULIN AND VESICULAR STOMATITIS VIRUS NUCLEOPROTEIN
Authors
:
M. G. Rudolph, J. A. Speir, A. Brunmark, N. Mattsson, M. R. Jackson, P. A. L. Teyton, I. A. Wilson
Date
:
03 Oct 00 (Deposition) - 28 Mar 01 (Release) - 13 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,P
Biol. Unit 1: A,B,P (1x)
Keywords
:
Major Histocompatibility Complex Peptide-Mhc, Immune System
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. G. Rudolph, J. A. Speir, A. Brunmark, N. Mattsson, M. R. Jackson, P. A. Peterson, L. Teyton, I. A. Wilson
The Crystal Structures Of K(Bm1) And K(Bm8) Reveal That Subtle Changes In The Peptide Environment Impact Thermostability And Alloreactivity.
Immunity V. 14 231 2001
[
close entry info
]
Hetero Components
(6, 10)
Info
All Hetero Components
1a: S-HYDROXYCYSTEINE (CSOa)
2a: BETA-L-FUCOSE (FULa)
3a: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDa)
3b: (4S)-2-METHYL-2,4-PENTANEDIOL (MPDb)
4a: (4R)-2-METHYLPENTANE-2,4-DIOL (MRDa)
5a: N-ACETYL-D-GLUCOSAMINE (NAGa)
5b: N-ACETYL-D-GLUCOSAMINE (NAGb)
5c: N-ACETYL-D-GLUCOSAMINE (NAGc)
6a: PHOSPHATE ION (PO4a)
6b: PHOSPHATE ION (PO4b)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CSO
1
Mod. Amino Acid
S-HYDROXYCYSTEINE
2
FUL
1
Ligand/Ion
BETA-L-FUCOSE
3
MPD
2
Ligand/Ion
(4S)-2-METHYL-2,4-PENTANEDIOL
4
MRD
1
Ligand/Ion
(4R)-2-METHYLPENTANE-2,4-DIOL
5
NAG
3
Ligand/Ion
N-ACETYL-D-GLUCOSAMINE
6
PO4
2
Ligand/Ion
PHOSPHATE ION
[
close Hetero Component info
]
Sites
(9, 9)
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)
9: AC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
GLU A:41 , ASN A:86
BINDING SITE FOR RESIDUE NAG A 500
2
AC2
SOFTWARE
ASN A:176 , NAG A:601 , FUL A:602 , HOH A:838 , HOH A:936 , HOH A:939
BINDING SITE FOR RESIDUE NAG A 600
3
AC3
SOFTWARE
NAG A:600 , FUL A:602
BINDING SITE FOR RESIDUE NAG A 601
4
AC4
SOFTWARE
GLN A:54 , LYS A:173 , ASN A:174 , NAG A:600 , NAG A:601 , HOH A:986
BINDING SITE FOR RESIDUE FUL A 602
5
AC5
SOFTWARE
ARG A:35 , ARG A:48 , MRD A:701 , GLU B:50 , MET B:51
BINDING SITE FOR RESIDUE PO4 A 801
6
AC6
SOFTWARE
PRO B:33 , HOH B:854
BINDING SITE FOR RESIDUE PO4 B 802
7
AC7
SOFTWARE
ILE A:23 , VAL A:25 , GLU A:32 , ARG A:35 , ASP A:37 , PO4 A:801 , SER B:52 , ASP B:53 , MET B:54
BINDING SITE FOR RESIDUE MRD A 701
8
AC8
SOFTWARE
ARG A:48 , ARG A:50 , ALA A:135 , ALA A:136 , ASP A:137
BINDING SITE FOR RESIDUE MPD A 702
9
AC9
SOFTWARE
TRP A:204 , SER B:11 , PRO B:14 , PRO B:15 , TRP B:95 , ASP B:96
BINDING SITE FOR RESIDUE MPD B 703
[
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 (D85D, chain B, )
5: 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_B2MG_MOUSE_004
*
R
101
T
B2MG_MOUSE
---
---
B
R
81
T
4
UniProt
VAR_B2MG_MOUSE_005
*
A
105
D
B2MG_MOUSE
---
---
B
D
85
D
5
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 (B:78-84,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.
SCOP Domains
(3, 3)
Info
All SCOP Domains
1a: SCOP_d1fzmb_ (B:)
2a: SCOP_d1fzma1 (A:182-274)
3a: SCOP_d1fzma2 (A: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
d1fzmb_
B:
Protein domain
:
Class I MHC, alpha-3 domain
(293)
Mouse (Mus musculus) [TaxId: 10090]
(102)
2a
d1fzma1
A:182-274
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)
3a
d1fzma2
A:1-181
[
close SCOP info
]
CATH Domains
(2, 3)
Info
all CATH domains
1a: CATH_1fzmA01 (A:1-181)
2a: CATH_1fzmB00 (B:1-99)
2b: CATH_1fzmA02 (A:182-273)
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
1fzmA01
A:1-181
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
House mouse (Mus musculus)
(616)
2a
1fzmB00
B:1-99
2b
1fzmA02
A:182-273
[
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 P
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 (78 KB)
Header - Asym.Unit
Biol.Unit 1 (73 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
1FZM
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
