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...
No precomputed SNP/Variant structure found.
Calculating the structure may take several minutes.
PLEASE WAIT...
Getting 'PROSITE' information from database.
2UYL
Biol. Unit 1
Info
Asym.Unit (268 KB)
Biol.Unit 1 (70 KB)
Biol.Unit 2 (70 KB)
Biol.Unit 3 (70 KB)
Biol.Unit 4 (70 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 MONOCLONAL ANTIBODY DIRECTED AGAINST AN ANTIGENIC DETERMINANT COMMON TO OGAWA AND INABA SEROTYPES OF VIBRIO CHOLERAE O1
Authors
:
F. Ahmed, A. Haouz, F. Nato, J. M. Fournier, P. M. Alzari
Date
:
10 Apr 07 (Deposition) - 13 May 08 (Release) - 06 Jun 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,M,N,V,W,X,Y
Biol. Unit 1: A,B (1x)
Biol. Unit 2: M,N (1x)
Biol. Unit 3: V,W (1x)
Biol. Unit 4: X,Y (1x)
Keywords
:
Fab Fragment, Monoclonal Antibody, Immune System, Immunoglobulin Domain, Immunoglobulin C Region, Anti-Lps Vibrio Cholerae
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Ahmed, G. Andre-Leroux, A. Haouz, A. Boutonnier, M. Delepierre, F. Qadri, F. Nato, J. M. Fournier, P. M. Alzari
Crystal Structure Of A Monoclonal Antibody Directed Against An Antigenic Determinant Common To Ogawa And Inaba Serotypes Of Vibrio Cholerae O1.
Proteins V. 70 284 2008
[
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
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: IG_MHC (A:197-203)
;
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.
IGKC_MOUSE
84-90
1
A:197-203
-
-
-
[
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_d2uyla2 (A:113-218)
1b: SCOP_d2uylm2 (M:113-216)
1c: SCOP_d2uylv2 (V:113-216)
1d: SCOP_d2uylx2 (X:113-216)
2a: SCOP_d2uylb1 (B:120-219)
2b: SCOP_d2uyln1 (N:120-219)
2c: SCOP_d2uylw1 (W:120-219)
2d: SCOP_d2uyly1 (Y:120-219)
3a: SCOP_d2uyla1 (A:1-112)
3b: SCOP_d2uylm1 (M:1-112)
3c: SCOP_d2uylv1 (V:1-112)
3d: SCOP_d2uylx1 (X:1-112)
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
:
automated matches
(652)
Mouse (Mus musculus) [TaxId: 10090]
(309)
1a
d2uyla2
A:113-218
1b
d2uylm2
M:113-216
1c
d2uylv2
V:113-216
1d
d2uylx2
X:113-216
Protein domain
:
Immunoglobulin heavy chain gamma constant domain 1, CH1-gamma
(608)
Mouse (Mus musculus) [TaxId: 10090]
(414)
2a
d2uylb1
B:120-219
2b
d2uyln1
N:120-219
2c
d2uylw1
W:120-219
2d
d2uyly1
Y:120-219
Family
:
V set domains (antibody variable domain-like)
(1919)
Protein domain
:
automated matches
(311)
Mouse (Mus musculus) [TaxId: 10090]
(112)
3a
d2uyla1
A:1-112
3b
d2uylm1
M:1-112
3c
d2uylv1
V:1-112
3d
d2uylx1
X:1-112
[
close SCOP info
]
CATH Domains
(1, 16)
Info
all CATH domains
1a: CATH_2uylA02 (A:115-214)
1b: CATH_2uylM02 (M:115-214)
1c: CATH_2uylV02 (V:115-214)
1d: CATH_2uylX02 (X:115-214)
1e: CATH_2uylA01 (A:1-113)
1f: CATH_2uylM01 (M:1-113)
1g: CATH_2uylV01 (V:1-113)
1h: CATH_2uylX01 (X:1-113)
1i: CATH_2uylB02 (B:120-218)
1j: CATH_2uylN02 (N:120-218)
1k: CATH_2uylW02 (W:120-218)
1l: CATH_2uylY02 (Y:120-218)
1m: CATH_2uylB01 (B:1-119)
1n: CATH_2uylN01 (N:1-119)
1o: CATH_2uylW01 (W:1-119)
1p: CATH_2uylY01 (Y:1-119)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Sandwich
(5577)
Topology
:
Immunoglobulin-like
(3897)
Homologous Superfamily
:
Immunoglobulins
(2282)
Mouse (Mus musculus)
(152)
1a
2uylA02
A:115-214
1b
2uylM02
M:115-214
1c
2uylV02
V:115-214
1d
2uylX02
X:115-214
1e
2uylA01
A:1-113
1f
2uylM01
M:1-113
1g
2uylV01
V:1-113
1h
2uylX01
X:1-113
1i
2uylB02
B:120-218
1j
2uylN02
N:120-218
1k
2uylW02
W:120-218
1l
2uylY02
Y:120-218
1m
2uylB01
B:1-119
1n
2uylN01
N:1-119
1o
2uylW01
W:1-119
1p
2uylY01
Y:1-119
[
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
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 (268 KB)
Header - Asym.Unit
Biol.Unit 1 (70 KB)
Header - Biol.Unit 1
Biol.Unit 2 (70 KB)
Header - Biol.Unit 2
Biol.Unit 3 (70 KB)
Header - Biol.Unit 3
Biol.Unit 4 (70 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
2UYL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help