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.
2XZL
Biol. Unit 1
Info
Asym.Unit (131 KB)
Biol.Unit 1 (123 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
UPF1-RNA COMPLEX
Authors
:
S. Chakrabarti, U. Jayachandran, F. Bonneau, F. Fiorini, C. Basquin, S H. Le Hir, E. Conti
Date
:
26 Nov 10 (Deposition) - 30 Mar 11 (Release) - 30 Mar 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.40
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A,B (1x)
Keywords
:
Hydrolase-Rna Complex, Nmd, Rna Degradation, Allosteric Regulation
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
S. Chakrabarti, U. Jayachandran, F. Bonneau, F. Fiorini, C. Basquin, S. Domcke, H. Le Hir, E. Conti
Molecular Mechanisms For The Rna-Dependent Atpase Activity Of Upf1 And Its Regulation By Upf2.
Mol. Cell V. 41 693 2011
[
close entry info
]
Hetero Components
(3, 14)
Info
All Hetero Components
1a: PENTAETHYLENE GLYCOL (1PEa)
1b: PENTAETHYLENE GLYCOL (1PEb)
1c: PENTAETHYLENE GLYCOL (1PEc)
1d: PENTAETHYLENE GLYCOL (1PEd)
1e: PENTAETHYLENE GLYCOL (1PEe)
1f: PENTAETHYLENE GLYCOL (1PEf)
1g: PENTAETHYLENE GLYCOL (1PEg)
1h: PENTAETHYLENE GLYCOL (1PEh)
1i: PENTAETHYLENE GLYCOL (1PEi)
1j: PENTAETHYLENE GLYCOL (1PEj)
1k: PENTAETHYLENE GLYCOL (1PEk)
1l: PENTAETHYLENE GLYCOL (1PEl)
2a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
3a: TETRAFLUOROALUMINATE ION (ALFa)
4a: MAGNESIUM ION (MGa)
5a: ZINC ION (ZNa)
5b: ZINC ION (ZNb)
5c: ZINC ION (ZNc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
1PE
12
Ligand/Ion
PENTAETHYLENE GLYCOL
2
ADP
1
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
3
ALF
1
Ligand/Ion
TETRAFLUOROALUMINATE ION
4
MG
-1
Ligand/Ion
MAGNESIUM ION
5
ZN
-1
Ligand/Ion
ZINC ION
[
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
CYS A:62 , CYS A:65 , CYS A:84 , HIS A:94
BINDING SITE FOR RESIDUE ZN A1851
02
AC2
SOFTWARE
CYS A:76 , CYS A:79 , HIS A:98 , HIS A:104
BINDING SITE FOR RESIDUE ZN A1852
03
AC3
SOFTWARE
CYS A:122 , CYS A:125 , CYS A:148 , CYS A:152
BINDING SITE FOR RESIDUE ZN A1853
04
AC4
SOFTWARE
GLN A:408 , GLN A:413 , GLY A:433 , THR A:434 , GLY A:435 , LYS A:436 , THR A:437 , VAL A:438 , TYR A:638 , ARG A:639 , GLU A:769 , ALF A:1855 , MG A:1856 , HOH A:2090 , HOH A:2091
BINDING SITE FOR RESIDUE ADP A1854
05
AC5
SOFTWARE
PRO A:432 , GLY A:433 , LYS A:436 , GLN A:601 , ARG A:639 , GLY A:767 , ARG A:801 , ADP A:1854 , MG A:1856 , HOH A:2047 , HOH A:2051
BINDING SITE FOR RESIDUE ALF A1855
06
AC6
SOFTWARE
THR A:437 , ADP A:1854 , ALF A:1855 , HOH A:2038 , HOH A:2047 , HOH A:2090
BINDING SITE FOR RESIDUE MG A1856
07
AC7
SOFTWARE
GLY A:377 , TYR A:381 , ARG A:678
BINDING SITE FOR RESIDUE 1PE A1857
08
AC8
SOFTWARE
GLY A:720 , LYS A:722 , GLN A:725 , ASP A:771 , TYR A:804
BINDING SITE FOR RESIDUE 1PE A1858
09
AC9
SOFTWARE
ALA A:369 , ILE A:370 , SER A:671 , LYS A:672 , PHE A:673 , TRP A:675 , PRO A:676 , ILE A:677 , ARG A:678 , 1PE A:1863
BINDING SITE FOR RESIDUE 1PE A1859
10
BC1
SOFTWARE
PHE A:647 , ASN A:650 , MET A:651 , HIS A:823 , HIS A:827
BINDING SITE FOR RESIDUE 1PE A1860
11
BC2
SOFTWARE
GLN A:362 , ASN A:841 , GLN A:843
BINDING SITE FOR RESIDUE 1PE A1861
12
BC3
SOFTWARE
ARG A:829 , LEU A:834 , LEU A:844 , CYS A:845 , VAL A:847 , LEU A:849 , HOH A:2086
BINDING SITE FOR RESIDUE 1PE A1862
13
BC4
SOFTWARE
ASN A:641 , ILE A:663 , THR A:667 , TRP A:675 , ILE A:677 , GLY A:679 , ILE A:680 , PRO A:681 , 1PE A:1859
BINDING SITE FOR RESIDUE 1PE A1863
14
BC5
SOFTWARE
HIS A:419 , ARG A:423 , LEU A:425 , SER A:426 , LEU A:427 , HIS A:629 , VAL A:630 , PRO A:631 , ILE A:632
BINDING SITE FOR RESIDUE 1PE A1864
15
BC6
SOFTWARE
PHE A:393 , HIS A:451 , ASP A:453 , LYS A:591 , GLN A:592
BINDING SITE FOR RESIDUE 1PE A1865
16
BC7
SOFTWARE
SER A:412 , ASN A:415 , ALA A:416 , ILE A:632 , ARG A:633
BINDING SITE FOR RESIDUE 1PE A1866
17
BC8
SOFTWARE
LYS A:367 , ASP A:371 , LYS A:373 , THR A:564 , LYS A:588
BINDING SITE FOR RESIDUE 1PE A1867
18
BC9
SOFTWARE
LYS A:372 , ILE A:375 , SER A:376 , GLY A:589
BINDING SITE FOR RESIDUE 1PE A1868
[
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
(, 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.
(no "Exon" information available for biological units yet)
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
(3, 3)
Info
all PFAM domains
1a: PFAM_AAA_11_2xzlA01 (A:408-609)
2a: PFAM_AAA_12_2xzlA02 (A:616-813)
3a: PFAM_UPF1_Zn_bind_2xzlA03 (A:60-208)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
AAA_11
(5)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(1)
1a
AAA_11-2xzlA01
A:408-609
Family
:
AAA_12
(5)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(1)
2a
AAA_12-2xzlA02
A:616-813
Clan
:
no clan defined [family: UPF1_Zn_bind]
(3)
Family
:
UPF1_Zn_bind
(3)
Saccharomyces cerevisiae (strain ATCC 204508 / S288c) (Bakers yeast)
(1)
3a
UPF1_Zn_bind-2xzlA03
A:60-208
[
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 (131 KB)
Header - Asym.Unit
Biol.Unit 1 (123 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
2XZL
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help