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.
3AH1
Asym. Unit
Info
Asym.Unit (108 KB)
Biol.Unit 1 (53 KB)
Biol.Unit 2 (54 KB)
Biol.Unit 3 (104 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
HA1 SUBCOMPONENT OF BOTULINUM TYPE C PROGENITOR TOXIN COMPLEXED WITH N-ACETYLNEURAMIC ACID
Authors
:
T. Nakamura, T. Tonozuka, A. Ide, T. Yuzawa, K. Oguma, A. Nishikawa
Date
:
13 Apr 10 (Deposition) - 28 Apr 10 (Release) - 28 Apr 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.20
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Toxin, Beta Trefoil, Hemagglutinin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
T. Nakamura, T. Tonozuka, A. Ide, T. Yuzawa, K. Oguma, A. Nishikawa
Sugar-Binding Sites Of The Ha1 Subcomponent Of Clostridium Botulinum Type C Progenitor Toxin
J. Mol. Biol. V. 376 854 2008
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(1, 3)
Info
All Hetero Components
1a: 5-N-ACETYL-BETA-D-NEURAMINIC ACID (SLBa)
1b: 5-N-ACETYL-BETA-D-NEURAMINIC ACID (SLBb)
1c: 5-N-ACETYL-BETA-D-NEURAMINIC ACID (SLBc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
SLB
3
Ligand/Ion
5-N-ACETYL-BETA-D-NEURAMINIC ACID
[
close Hetero Component info
]
Sites
(3, 3)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ASN A:24 , LYS A:40 , GLU A:145 , ALA A:146 , LYS A:166 , ASN A:167 , LEU A:168 , TRP A:176 , PHE A:179 , ARG A:183 , HOH A:305 , HOH A:353
BINDING SITE FOR RESIDUE SLB A 2000
2
AC2
SOFTWARE
ARG A:10 , ASN A:12 , GLU A:13 , ASN A:232 , TYR A:246 , THR A:251 , PRO B:76 , LEU B:77 , SER B:78 , HOH B:345
BINDING SITE FOR RESIDUE SLB A 2002
3
AC3
SOFTWARE
TRP A:38 , LEU A:41 , SER A:182 , GLU A:203 , HOH A:310 , LYS B:166 , ASN B:167 , LEU B:168 , TRP B:176 , PHE B:179 , ARG B:183 , HOH B:430
BINDING SITE FOR RESIDUE SLB B 2001
[
close Site info
]
SAPs(SNPs)/Variants
(13, 26)
Info
(mutated residues are not available)
All SNPs/Variants
01: VAR_HA33_CLOBO_001 (N22S, chain A/B, )
02: VAR_HA33_CLOBO_002 (K60T, chain A/B, )
03: VAR_HA33_CLOBO_003 (N74D, chain A/B, )
04: VAR_HA33_CLOBO_004 (N98D, chain A/B, )
05: VAR_HA33_CLOBO_005 (I106L, chain A/B, )
06: VAR_HA33_CLOBO_006 (I120T, chain A/B, )
07: VAR_HA33_CLOBO_007 (M125I, chain A/B, )
08: VAR_HA33_CLOBO_008 (S131N, chain A/B, )
09: VAR_HA33_CLOBO_009 (S133N, chain A/B, )
10: VAR_HA33_CLOBO_010 (I187L, chain A/B, )
11: VAR_HA33_CLOBO_011 (I187T, chain A/B, )
12: VAR_HA33_CLOBO_012 (I262T, chain A/B, )
13: VAR_HA33_CLOBO_013 (H267N, chain A/B, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
01
UniProt
VAR_HA33_CLOBO_001
*
N
22
S
HA33_CLOBO
---
---
A/B
N
22
S
02
UniProt
VAR_HA33_CLOBO_002
*
K
60
T
HA33_CLOBO
---
---
A/B
K
60
T
03
UniProt
VAR_HA33_CLOBO_003
*
N
74
D
HA33_CLOBO
---
---
A/B
N
74
D
04
UniProt
VAR_HA33_CLOBO_004
*
N
98
D
HA33_CLOBO
---
---
A/B
N
98
D
05
UniProt
VAR_HA33_CLOBO_005
*
I
106
L
HA33_CLOBO
---
---
A/B
I
106
L
06
UniProt
VAR_HA33_CLOBO_006
*
I
120
T
HA33_CLOBO
---
---
A/B
I
120
T
07
UniProt
VAR_HA33_CLOBO_007
*
M
125
I
HA33_CLOBO
---
---
A/B
M
125
I
08
UniProt
VAR_HA33_CLOBO_008
*
S
131
N
HA33_CLOBO
---
---
A/B
S
131
N
09
UniProt
VAR_HA33_CLOBO_009
*
S
133
N
HA33_CLOBO
---
---
A/B
S
133
N
10
UniProt
VAR_HA33_CLOBO_010
*
I
187
L
HA33_CLOBO
---
---
A/B
I
187
L
11
UniProt
VAR_HA33_CLOBO_011
*
I
187
T
HA33_CLOBO
---
---
A/B
I
187
T
12
UniProt
VAR_HA33_CLOBO_012
*
I
262
T
HA33_CLOBO
---
---
A/B
I
262
T
13
UniProt
VAR_HA33_CLOBO_013
*
H
267
N
HA33_CLOBO
---
---
A/B
H
267
N
* 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: RICIN_B_LECTIN (A:12-140,B:12-140|A:180-284,B:180-...)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RICIN_B_LECTIN
PS50231
Lectin domain of ricin B chain profile.
HA33_CLOBO
12-140
180-284
4
A:12-140
B:12-140
A:180-284
B:180-284
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3ah1a1 (A:4-148)
1b: SCOP_d3ah1b1 (B:-1-148)
1c: SCOP_d3ah1b2 (B:149-286)
1d: SCOP_d3ah1a2 (A:149-286)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
All beta proteins
(24004)
Fold
:
beta-Trefoil
(385)
Superfamily
:
Ricin B-like lectins
(91)
Family
:
Ricin B-like
(65)
Protein domain
:
Hemagglutinin component Ha1
(4)
Clostridium botulinum [TaxId: 1491]
(3)
1a
d3ah1a1
A:4-148
1b
d3ah1b1
B:-1-148
1c
d3ah1b2
B:149-286
1d
d3ah1a2
A:149-286
[
close SCOP info
]
CATH Domains
(1, 4)
Info
all CATH domains
1a: CATH_3ah1B01 (B:-1-141)
1b: CATH_3ah1A02 (A:142-286)
1c: CATH_3ah1B02 (B:142-286)
1d: CATH_3ah1A01 (A:4-141)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Mainly Beta
(13760)
Architecture
:
Trefoil
(289)
Topology
:
Trefoil (Acidic Fibroblast Growth Factor, subunit A)
(289)
Homologous Superfamily
:
[code=2.80.10.50, no name defined]
(289)
Clostridium botulinum. Organism_taxid: 1491. Strain: type c.
(3)
1a
3ah1B01
B:-1-141
1b
3ah1A02
A:142-286
1c
3ah1B02
B:142-286
1d
3ah1A01
A:4-141
[
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 (108 KB)
Header - Asym.Unit
Biol.Unit 1 (53 KB)
Header - Biol.Unit 1
Biol.Unit 2 (54 KB)
Header - Biol.Unit 2
Biol.Unit 3 (104 KB)
Header - Biol.Unit 3
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
3AH1
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
