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.
PLEASE WAIT...
Getting 'Exon' information from database.
3LIM
Asym. Unit
Info
Asym.Unit (206 KB)
Biol.Unit 1 (37 KB)
Biol.Unit 2 (37 KB)
Biol.Unit 3 (37 KB)
Biol.Unit 4 (36 KB)
Biol.Unit 5 (36 KB)
Biol.Unit 6 (36 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 THE PORE FORMING TOXIN FRAC FROM SEA ANEMONE ACTINIA FRAGACEA
Authors
:
A. E. Mechaly, A. Bellomio, K. Morante, J. M. Gonzalez-Manas, D. M. A. Gu
Date
:
25 Jan 10 (Deposition) - 15 Dec 10 (Release) - 20 Jul 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.80
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Biol. Unit 5: E (1x)
Biol. Unit 6: F (1x)
Keywords
:
Pore Forming Toxin, Actinoporins, Toxin
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. E. Mechaly, A. Bellomio, D. Gil-Carton, K. Morante, M. Valle, J. M. Gonzalez-Manas, D. M. Guerin
Structural Insights Into The Oligomerization And Architecture Of Eukaryotic Membrane Pore-Forming Toxins.
Structure V. 19 181 2011
[
close entry info
]
Hetero Components
(1, 18)
Info
All Hetero Components
1a: LAURYL DIMETHYLAMINE-N-OXIDE (LDAa)
1b: LAURYL DIMETHYLAMINE-N-OXIDE (LDAb)
1c: LAURYL DIMETHYLAMINE-N-OXIDE (LDAc)
1d: LAURYL DIMETHYLAMINE-N-OXIDE (LDAd)
1e: LAURYL DIMETHYLAMINE-N-OXIDE (LDAe)
1f: LAURYL DIMETHYLAMINE-N-OXIDE (LDAf)
1g: LAURYL DIMETHYLAMINE-N-OXIDE (LDAg)
1h: LAURYL DIMETHYLAMINE-N-OXIDE (LDAh)
1i: LAURYL DIMETHYLAMINE-N-OXIDE (LDAi)
1j: LAURYL DIMETHYLAMINE-N-OXIDE (LDAj)
1k: LAURYL DIMETHYLAMINE-N-OXIDE (LDAk)
1l: LAURYL DIMETHYLAMINE-N-OXIDE (LDAl)
1m: LAURYL DIMETHYLAMINE-N-OXIDE (LDAm)
1n: LAURYL DIMETHYLAMINE-N-OXIDE (LDAn)
1o: LAURYL DIMETHYLAMINE-N-OXIDE (LDAo)
1p: LAURYL DIMETHYLAMINE-N-OXIDE (LDAp)
1q: LAURYL DIMETHYLAMINE-N-OXIDE (LDAq)
1r: LAURYL DIMETHYLAMINE-N-OXIDE (LDAr)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
LDA
18
Ligand/Ion
LAURYL DIMETHYLAMINE-N-OXIDE
[
close Hetero Component info
]
Sites
(18, 18)
Info
All Sites
01: AC1 (SOFTWARE)
02: AC2 (SOFTWARE)
03: AC3 (SOFTWARE)
04: AC4 (SOFTWARE)
05: AC5 (SOFTWARE)
06: AC6 (SOFTWARE)
07: AC7 (SOFTWARE)
08: AC8 (SOFTWARE)
09: AC9 (SOFTWARE)
10: BC1 (SOFTWARE)
11: BC2 (SOFTWARE)
12: BC3 (SOFTWARE)
13: BC4 (SOFTWARE)
14: BC5 (SOFTWARE)
15: BC6 (SOFTWARE)
16: BC7 (SOFTWARE)
17: BC8 (SOFTWARE)
18: BC9 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG A:53 , GLN A:130 , TYR A:133 , TYR A:137 , TYR A:138 , LDA A:202 , HOH A:438
BINDING SITE FOR RESIDUE LDA A 201
02
AC2
SOFTWARE
TYR A:51 , PHE A:52 , ARG A:53 , LDA A:201
BINDING SITE FOR RESIDUE LDA A 202
03
AC3
SOFTWARE
ASN A:111 , TRP A:112 , TYR E:110 , ASN E:111 , LDA E:203
BINDING SITE FOR RESIDUE LDA A 203
04
AC4
SOFTWARE
ARG B:53 , TYR B:113 , GLN B:130 , TYR B:133 , TYR B:137 , TYR B:138 , LDA B:202 , HOH B:642
BINDING SITE FOR RESIDUE LDA B 201
05
AC5
SOFTWARE
TYR B:51 , PHE B:52 , ARG B:53 , GLN B:130 , LDA B:201
BINDING SITE FOR RESIDUE LDA B 202
06
AC6
SOFTWARE
TRP B:112 , TYR D:110 , ASN D:111 , LDA D:203
BINDING SITE FOR RESIDUE LDA B 203
07
AC7
SOFTWARE
ARG C:53 , TYR C:113 , GLN C:130 , TYR C:133 , TYR C:137 , TYR C:138 , LDA C:202 , HOH C:289
BINDING SITE FOR RESIDUE LDA C 201
08
AC8
SOFTWARE
TYR C:51 , PHE C:52 , ARG C:53 , LDA C:201
BINDING SITE FOR RESIDUE LDA C 202
09
AC9
SOFTWARE
ASN C:111 , TRP C:112 , TYR F:110 , ASN F:111 , LDA F:203
BINDING SITE FOR RESIDUE LDA C 203
10
BC1
SOFTWARE
ARG D:53 , TYR D:113 , GLN D:130 , TYR D:133 , TYR D:137 , TYR D:138
BINDING SITE FOR RESIDUE LDA D 201
11
BC2
SOFTWARE
TYR D:51 , PHE D:52 , ARG D:53
BINDING SITE FOR RESIDUE LDA D 202
12
BC3
SOFTWARE
ASN B:111 , LDA B:203 , TRP D:112
BINDING SITE FOR RESIDUE LDA D 203
13
BC4
SOFTWARE
ARG E:53 , TYR E:113 , GLN E:130 , TYR E:133 , TYR E:137 , TYR E:138 , LDA E:202 , HOH E:530
BINDING SITE FOR RESIDUE LDA E 201
14
BC5
SOFTWARE
TYR E:51 , ARG E:53 , GLN E:130 , GLU E:134 , LDA E:201
BINDING SITE FOR RESIDUE LDA E 202
15
BC6
SOFTWARE
TYR A:110 , ASN A:111 , LDA A:203 , TRP E:112
BINDING SITE FOR RESIDUE LDA E 203
16
BC7
SOFTWARE
ARG F:53 , TYR F:113 , GLN F:130 , TYR F:133 , TYR F:137 , TYR F:138 , LDA F:202
BINDING SITE FOR RESIDUE LDA F 201
17
BC8
SOFTWARE
TYR F:51 , PHE F:52 , ARG F:53 , GLU F:134 , LDA F:201
BINDING SITE FOR RESIDUE LDA F 202
18
BC9
SOFTWARE
TYR C:110 , ASN C:111 , LDA C:203 , ASN F:111 , TRP F:112
BINDING SITE FOR RESIDUE LDA F 203
[
close Site info
]
SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are not available)
All SNPs/Variants
View:
Select:
Label:
Sorry, no Info available
[
close SNP/Variant info
]
PROSITE Patterns/Profiles
(0, 0)
Info
All PROSITE Patterns/Profiles
;
View:
Select:
Label:
End label:
Sorry, no Info available
[
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
(0, 0)
Info
All SCOP Domains
View:
Select:
Label:
Sorry, no Info available
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Anemone_cytotox_3limF01 (F:3-178)
1b: PFAM_Anemone_cytotox_3limF02 (F:3-178)
1c: PFAM_Anemone_cytotox_3limF03 (F:3-178)
1d: PFAM_Anemone_cytotox_3limF04 (F:3-178)
1e: PFAM_Anemone_cytotox_3limF05 (F:3-178)
1f: PFAM_Anemone_cytotox_3limF06 (F:3-178)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
no clan defined [family: Anemone_cytotox]
(3)
Family
:
Anemone_cytotox
(3)
Actinia fragacea (Strawberry anemone)
(1)
1a
Anemone_cytotox-3limF01
F:3-178
1b
Anemone_cytotox-3limF02
F:3-178
1c
Anemone_cytotox-3limF03
F:3-178
1d
Anemone_cytotox-3limF04
F:3-178
1e
Anemone_cytotox-3limF05
F:3-178
1f
Anemone_cytotox-3limF06
F:3-178
[
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 D
Chain E
Chain F
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 (206 KB)
Header - Asym.Unit
Biol.Unit 1 (37 KB)
Header - Biol.Unit 1
Biol.Unit 2 (37 KB)
Header - Biol.Unit 2
Biol.Unit 3 (37 KB)
Header - Biol.Unit 3
Biol.Unit 4 (36 KB)
Header - Biol.Unit 4
Biol.Unit 5 (36 KB)
Header - Biol.Unit 5
Biol.Unit 6 (36 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
3LIM
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
