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.
2ZUF
Asym. Unit
Info
Asym.Unit (145 KB)
Biol.Unit 1 (107 KB)
Biol.Unit 2 (37 KB)
Biol.Unit 3 (141 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 PYROCOCCUS HORIKOSHII ARGINYL-TRNA SYNTHETASE COMPLEXED WITH TRNA(ARG)
Authors
:
M. Konno, T. Sumida, E. Uchikawa, Y. Mori, T. Yanagisawa, S. Sekine, S. Yokoyama
Date
:
16 Oct 08 (Deposition) - 18 Aug 09 (Release) - 18 Aug 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.30
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Rrs/Trna(Arg), Aminoacyl-Trna Synthetase, Atp-Binding, Cytoplasm, Ligase, Nucleotide-Binding, Protein Biosynthesis, Ligase/Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Konno, T. Sumida, E. Uchikawa, Y. Mori, T. Yanagisawa, S. Sekine, S. Yokoyama
Modeling Of Trna-Assisted Mechanism Of Arg Activation Based On A Structure Of Arg-Trna Synthetase, Trna, And An Atp Analog (Anp)
Febs J. V. 276 4763 2009
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(0, 0)
Info
All Sites
View:
Select:
Label:
Sorry, no Info available
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: AA_TRNA_LIGASE_I (A:130-139)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
AA_TRNA_LIGASE_I
PS00178
Aminoacyl-transfer RNA synthetases class-I signature.
SYR_PYRHO
130-139
1
A:130-139
[
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
(2, 2)
Info
all CATH domains
1a: CATH_2zufA02 (A:117-510)
2a: CATH_2zufA03 (A:511-629)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
Tyrosyl-Transfer RNA Synthetase , subunit E, domain 1
(328)
Pyrococcus horikoshii. Organism_taxid: 53953.
(2)
1a
2zufA02
A:117-510
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Isoleucyl-tRNA Synthetase; Domain 1
(35)
Homologous Superfamily
:
Isoleucyl-tRNA Synthetase; Domain 1
(35)
Pyrococcus horikoshii. Organism_taxid: 53953.
(2)
2a
2zufA03
A:511-629
[
close CATH info
]
Pfam Domains
(3, 4)
Info
all PFAM domains
1a: PFAM_DALR_1_2zufA01 (A:507-629)
2a: PFAM_tRNA_synt_1d_2zufA02 (A:368-493)
2b: PFAM_tRNA_synt_1d_2zufA03 (A:368-493)
3a: PFAM_Arg_tRNA_synt_N_2zufA04 (A:4-90)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
DALR
(5)
Family
:
DALR_1
(2)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
(2)
1a
DALR_1-2zufA01
A:507-629
Clan
:
HUP
(230)
Family
:
tRNA-synt_1d
(2)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
(2)
2a
tRNA-synt_1d-2zufA02
A:368-493
2b
tRNA-synt_1d-2zufA03
A:368-493
Clan
:
no clan defined [family: Arg_tRNA_synt_N]
(2)
Family
:
Arg_tRNA_synt_N
(2)
Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM 9974 / NBRC 100139 / OT-3)
(2)
3a
Arg_tRNA_synt_N-2zufA04
A:4-90
[
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 (145 KB)
Header - Asym.Unit
Biol.Unit 1 (107 KB)
Header - Biol.Unit 1
Biol.Unit 2 (37 KB)
Header - Biol.Unit 2
Biol.Unit 3 (141 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
2ZUF
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
