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.
4TSN
Asym. Unit
Info
Asym.Unit (259 KB)
Biol.Unit 1 (67 KB)
Biol.Unit 2 (65 KB)
Biol.Unit 3 (66 KB)
Biol.Unit 4 (66 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 FRAC WITH POC BOUND (CRYSTAL FORM II)
Authors
:
J. M. M. Caaveiro, K. Tanaka, K. Tsumoto
Date
:
19 Jun 14 (Deposition) - 04 Mar 15 (Release) - 03 Aug 16 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.57
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: C (1x)
Biol. Unit 4: D (1x)
Keywords
:
Toxin, Actinoporin, Pore-Forming Toxin, Membrane Lipids, Phosphocholine, Lipid-Protein Interaction
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
K. Tanaka, J. M. M. Caaveiro, K. Morante, J. M. Gonzalez-Manas, K. Tsumoto
Structural Basis For Self-Assembly Of A Cytolytic Pore Line By Protein And Lipid
Nat Commun V. 6 6337 2015
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(4, 23)
Info
All Hetero Components
1a: ACETATE ION (ACTa)
1b: ACETATE ION (ACTb)
2a: GLYCEROL (GOLa)
3a: PHOSPHOCHOLINE (PCa)
3b: PHOSPHOCHOLINE (PCb)
3c: PHOSPHOCHOLINE (PCc)
3d: PHOSPHOCHOLINE (PCd)
3e: PHOSPHOCHOLINE (PCe)
3f: PHOSPHOCHOLINE (PCf)
3g: PHOSPHOCHOLINE (PCg)
3h: PHOSPHOCHOLINE (PCh)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ACT
2
Ligand/Ion
ACETATE ION
2
GOL
1
Ligand/Ion
GLYCEROL
3
PC
8
Ligand/Ion
PHOSPHOCHOLINE
4
SO4
12
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(23, 23)
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: AD1 (SOFTWARE)
11: AD2 (SOFTWARE)
12: AD3 (SOFTWARE)
13: AD4 (SOFTWARE)
14: AD5 (SOFTWARE)
15: AD6 (SOFTWARE)
16: AD7 (SOFTWARE)
17: AD8 (SOFTWARE)
18: AD9 (SOFTWARE)
19: AE1 (SOFTWARE)
20: AE2 (SOFTWARE)
21: AE3 (SOFTWARE)
22: AE4 (SOFTWARE)
23: AE5 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
SER A:54 , THR A:84 , GLY A:85 , SER A:105 , PRO A:107 , TYR A:108 , TYR A:113 , TYR A:133 , TYR A:137 , TYR A:138 , HOH A:303 , HOH A:318 , HOH A:348
binding site for residue PC A 201
02
AC2
SOFTWARE
TYR A:113 , SER A:114 , TRP A:116 , TYR A:137 , PRO A:142 , GOL A:206 , HOH A:304
binding site for residue PC A 202
03
AC3
SOFTWARE
TRP A:112 , TYR A:113
binding site for residue PC A 203
04
AC4
SOFTWARE
ARG A:120 , TYR A:122 , LYS A:123 , HOH A:366 , HOH A:401
binding site for residue SO4 A 204
05
AC5
SOFTWARE
LYS A:30 , ARG A:31 , HOH A:305 , HOH A:377 , HOH A:454
binding site for residue SO4 A 205
06
AC6
SOFTWARE
TRP A:112 , TYR A:113 , SER A:114 , ARG A:144 , PC A:202 , HOH A:302
binding site for residue GOL A 206
07
AC7
SOFTWARE
ARG B:53 , SER B:54 , THR B:84 , GLY B:85 , SER B:105 , PRO B:107 , TYR B:108 , TYR B:113 , TYR B:133 , TYR B:137 , TYR B:138 , HOH B:302 , HOH B:325 , HOH B:352
binding site for residue PC B 201
08
AC8
SOFTWARE
TYR B:113 , SER B:114 , TRP B:116 , TYR B:137 , HOH B:311 , HOH B:394
binding site for residue PC B 202
09
AC9
SOFTWARE
LYS A:30 , TYR A:108 , HOH A:307 , ARG B:120 , TYR B:122 , LYS B:123 , HOH B:303 , HOH B:313
binding site for residue SO4 B 203
10
AD1
SOFTWARE
ARG B:144 , HOH B:439 , GLY D:124 , GLN D:125
binding site for residue SO4 B 204
11
AD2
SOFTWARE
ASP A:109 , TRP A:112 , LYS B:123
binding site for residue ACT B 205
12
AD3
SOFTWARE
ARG C:53 , SER C:54 , GLY C:85 , SER C:105 , PRO C:107 , TYR C:108 , TYR C:113 , TYR C:133 , TYR C:137 , TYR C:138 , SO4 C:202 , HOH C:301 , HOH C:311 , HOH C:351
binding site for residue PC C 201
13
AD4
SOFTWARE
ARG C:53 , GLN C:130 , TYR C:133 , TYR C:138 , PC C:201
binding site for residue SO4 C 202
14
AD5
SOFTWARE
VAL C:29 , LYS C:30 , LYS C:77 , ARG C:79 , GLY C:80 , HOH C:303 , HOH C:306 , HOH C:377 , HOH D:334
binding site for residue SO4 C 203
15
AD6
SOFTWARE
ARG C:120 , TYR C:122 , LYS C:123 , HOH C:413 , HOH C:441
binding site for residue SO4 C 204
16
AD7
SOFTWARE
ARG D:53 , SER D:54 , GLY D:85 , SER D:105 , PRO D:107 , TYR D:108 , TYR D:113 , TYR D:133 , TYR D:137 , TYR D:138 , SO4 D:203 , HOH D:304 , HOH D:330 , HOH D:372
binding site for residue PC D 201
17
AD8
SOFTWARE
TRP D:112 , TYR D:113 , SER D:114 , TRP D:116 , TYR D:137 , PRO D:142 , HOH D:390
binding site for residue PC D 202
18
AD9
SOFTWARE
ARG D:53 , GLN D:130 , TYR D:133 , TYR D:138 , PC D:201
binding site for residue SO4 D 203
19
AE1
SOFTWARE
ASN D:28 , VAL D:29 , LYS D:30 , LYS D:77 , ARG D:79 , GLY D:80 , HOH D:337 , HOH D:343
binding site for residue SO4 D 204
20
AE2
SOFTWARE
THR B:56 , ASN B:78 , ARG B:79 , SER D:167 , HOH D:318 , HOH D:336
binding site for residue SO4 D 205
21
AE3
SOFTWARE
ARG C:79 , ARG D:120 , TYR D:122 , LYS D:123 , HOH D:405
binding site for residue SO4 D 206
22
AE4
SOFTWARE
LYS D:178
binding site for residue SO4 D 207
23
AE5
SOFTWARE
ASN D:28 , ARG D:79
binding site for residue ACT D 208
[
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
(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 C
Chain D
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 (259 KB)
Header - Asym.Unit
Biol.Unit 1 (67 KB)
Header - Biol.Unit 1
Biol.Unit 2 (65 KB)
Header - Biol.Unit 2
Biol.Unit 3 (66 KB)
Header - Biol.Unit 3
Biol.Unit 4 (66 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
4TSN
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
