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.
3ZL5
Asym. Unit
Info
Asym.Unit (273 KB)
Biol.Unit 1 (262 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 SCHISTOSOMA MANSONI PEROXIREDOXIN I C48S MUTANT WITH ONE DECAMER IN THE ASU
Authors
:
F. Saccoccia, F. Angelucci, M. Ardini, G. Boumis, M. Brunori, L. Dilean R. Ippoliti, A. E. Miele, G. Natoli, S. Scotti, A. Bellelli
Date
:
28 Jan 13 (Deposition) - 11 Sep 13 (Release) - 13 Nov 13 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.49
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J
Biol. Unit 1: A,B,C,D,E,F,G,H,I,J (1x)
Keywords
:
Oxidoreductase, Peroxidase, Schistosomiasis, Chaperone, Thioredoxin Fold
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
F. Angelucci, F. Saccoccia, M. Ardini, G. Boumis, M. Brunori, L. Dileandro, R. Ippoliti, A. E. Miele, G. Natoli, S. Scotti, A. Bellelli
Switching Between The Alternative Structures And Functions Of A 2-Cys Peroxiredoxin, By Site-Directed Mutagenesis
J. Mol. Biol. V. 425 4556 2013
[
close entry info
]
Hetero Components
(2, 16)
Info
All Hetero Components
1a: DI(HYDROXYETHYL)ETHER (PEGa)
1b: DI(HYDROXYETHYL)ETHER (PEGb)
1c: DI(HYDROXYETHYL)ETHER (PEGc)
1d: DI(HYDROXYETHYL)ETHER (PEGd)
2a: SULFATE ION (SO4a)
2b: SULFATE ION (SO4b)
2c: SULFATE ION (SO4c)
2d: SULFATE ION (SO4d)
2e: SULFATE ION (SO4e)
2f: SULFATE ION (SO4f)
2g: SULFATE ION (SO4g)
2h: SULFATE ION (SO4h)
2i: SULFATE ION (SO4i)
2j: SULFATE ION (SO4j)
2k: SULFATE ION (SO4k)
2l: SULFATE ION (SO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
PEG
4
Ligand/Ion
DI(HYDROXYETHYL)ETHER
2
SO4
12
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(16, 16)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
THR A:45 , PHE A:46 , VAL A:47 , SER A:48 , ARG A:124
BINDING SITE FOR RESIDUE SO4 A1165
02
AC2
SOFTWARE
THR C:45 , SER C:48 , ARG C:124
BINDING SITE FOR RESIDUE SO4 C1165
03
AC3
SOFTWARE
THR H:45 , PHE H:46 , VAL H:47 , SER H:48 , ARG H:124
BINDING SITE FOR RESIDUE SO4 H1164
04
AC4
SOFTWARE
PRO J:41 , THR J:45 , PHE J:46 , VAL J:47 , SER J:48 , ARG J:124 , LYS J:143 , SO4 J:1166
BINDING SITE FOR RESIDUE SO4 J1165
05
AC5
SOFTWARE
TYR A:78 , ASN J:121 , SO4 J:1165
BINDING SITE FOR RESIDUE SO4 J1166
06
AC6
SOFTWARE
THR I:45 , PHE I:46 , VAL I:47 , SER I:48 , ARG I:124 , HOH I:2005 , HOH I:2019
BINDING SITE FOR RESIDUE SO4 I1164
07
AC7
SOFTWARE
ASP I:87 , ARG I:88 , LYS I:89 , SO4 I:1166
BINDING SITE FOR RESIDUE SO4 I1165
08
AC8
SOFTWARE
THR E:45 , PHE E:46 , VAL E:47 , SER E:48 , ARG E:124 , HOH E:2009
BINDING SITE FOR RESIDUE SO4 E1164
09
AC9
SOFTWARE
THR D:45 , PHE D:46 , VAL D:47 , SER D:48 , ARG D:124 , HOH D:2011
BINDING SITE FOR RESIDUE SO4 D1165
10
BC1
SOFTWARE
THR F:45 , PHE F:46 , VAL F:47 , SER F:48 , ARG F:124 , PEG F:1166
BINDING SITE FOR RESIDUE SO4 F1164
11
BC2
SOFTWARE
THR G:45 , PHE G:46 , VAL G:47 , SER G:48 , ARG G:124
BINDING SITE FOR RESIDUE SO4 G1164
12
BC3
SOFTWARE
TYR E:78 , LYS I:89 , SO4 I:1165 , HOH I:2024
BINDING SITE FOR RESIDUE SO4 I1166
13
BC4
SOFTWARE
GLU E:151 , LEU E:155 , THR F:139 , ARG F:147 , SER F:148 , GLU F:151 , THR F:152 , LEU F:155
BINDING SITE FOR RESIDUE PEG F1165
14
BC5
SOFTWARE
TYR H:78 , ASP I:119 , ASN I:121 , LYS I:143
BINDING SITE FOR RESIDUE PEG I1167
15
BC6
SOFTWARE
VAL H:2 , LEU H:3 , LEU H:4 , ARG H:7 , PRO H:8
BINDING SITE FOR RESIDUE PEG H1165
16
BC7
SOFTWARE
PHE F:46 , SO4 F:1164
BINDING SITE FOR RESIDUE PEG F1166
[
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
(1, 10)
Info
All SCOP Domains
1a: SCOP_d3zl5a_ (A:)
1b: SCOP_d3zl5d_ (D:)
1c: SCOP_d3zl5e_ (E:)
1d: SCOP_d3zl5f_ (F:)
1e: SCOP_d3zl5g_ (G:)
1f: SCOP_d3zl5h_ (H:)
1g: SCOP_d3zl5i_ (I:)
1h: SCOP_d3zl5j_ (J:)
1i: SCOP_d3zl5b_ (B:)
1j: SCOP_d3zl5c_ (C:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Thioredoxin fold
(994)
Superfamily
:
Thioredoxin-like
(992)
Family
:
automated matches
(347)
Protein domain
:
automated matches
(347)
Blood fluke (Schistosoma mansoni) [TaxId: 6183]
(9)
1a
d3zl5a_
A:
1b
d3zl5d_
D:
1c
d3zl5e_
E:
1d
d3zl5f_
F:
1e
d3zl5g_
G:
1f
d3zl5h_
H:
1g
d3zl5i_
I:
1h
d3zl5j_
J:
1i
d3zl5b_
B:
1j
d3zl5c_
C:
[
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
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
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 (273 KB)
Header - Asym.Unit
Biol.Unit 1 (262 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
3ZL5
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help