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.
1HC7
Biol. Unit 1
Info
Asym.Unit (323 KB)
Biol.Unit 1 (161 KB)
Biol.Unit 2 (162 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
PROLYL-TRNA SYNTHETASE FROM THERMUS THERMOPHILUS
Authors
:
A. Yaremchuk, M. Tukalo, S. Cusack
Date
:
26 Apr 01 (Deposition) - 18 Jun 01 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.43
Chains
:
Asym. Unit : A,B,C,D
Biol. Unit 1: A,B (1x)
Biol. Unit 2: C,D (1x)
Keywords
:
Aminoacyl-Trna Synthetase, Atp + L-Proline + Trna(Pro) Amp + Ppi + L-Prolyl-Trna(Pro), Class Ii Aminoacyl-Trna Synthetase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
A. Yaremchuk, M. Tukalo, M. Grotli, S. Cusack
A Succession Of Substrate Induced Conformational Changes Ensures The Amino Acid Specificity Of Thermus Thermophilus Prolyl-Trna Synthetase: Comparison With Histidyl-Trna Synthetase
J. Mol. Biol. V. 309 989 2001
(for further references see the
PDB file header
)
[
close entry info
]
Hetero Components
(0, 0)
Info
All Hetero Components
1a: ZINC ION (ZNa)
1b: ZINC ION (ZNb)
1c: ZINC ION (ZNc)
1d: ZINC ION (ZNd)
View:
Select:
Label:
Sorry, no Info available
[
close Hetero component info
]
Sites
(2, 2)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
CYS A:427 , CYS A:432 , CYS A:458 , CYS A:461
BINDING SITE FOR RESIDUE ZN A 490
2
AC2
SOFTWARE
CYS B:427 , CYS B:432 , CYS B:458 , CYS B:461
BINDING SITE FOR RESIDUE ZN B 490
[
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
(3, 12)
Info
All SCOP Domains
1a: SCOP_d1hc7a2 (A:5-276)
1b: SCOP_d1hc7b2 (B:5-276)
1c: SCOP_d1hc7c2 (C:5-276)
1d: SCOP_d1hc7d2 (D:5-276)
2a: SCOP_d1hc7a3 (A:404-477)
2b: SCOP_d1hc7b3 (B:404-477)
2c: SCOP_d1hc7c3 (C:404-477)
2d: SCOP_d1hc7d3 (D:404-477)
3a: SCOP_d1hc7a1 (A:277-403)
3b: SCOP_d1hc7b1 (B:277-403)
3c: SCOP_d1hc7c1 (C:277-403)
3d: SCOP_d1hc7d1 (D:277-403)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Class II aaRS and biotin synthetases
(165)
Superfamily
:
Class II aaRS and biotin synthetases
(165)
Family
:
Class II aminoacyl-tRNA synthetase (aaRS)-like, catalytic domain
(103)
Protein domain
:
Prolyl-tRNA synthetase (ProRS)
(9)
Thermus thermophilus [TaxId: 274]
(4)
1a
d1hc7a2
A:5-276
1b
d1hc7b2
B:5-276
1c
d1hc7c2
C:5-276
1d
d1hc7d2
D:5-276
Fold
:
IF3-like
(127)
Superfamily
:
C-terminal domain of ProRS
(9)
Family
:
C-terminal domain of ProRS
(9)
Protein domain
:
C-terminal domain of ProRS
(9)
Thermus thermophilus [TaxId: 274]
(4)
2a
d1hc7a3
A:404-477
2b
d1hc7b3
B:404-477
2c
d1hc7c3
C:404-477
2d
d1hc7d3
D:404-477
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
Anticodon-binding domain-like
(97)
Superfamily
:
Class II aaRS ABD-related
(40)
Family
:
Anticodon-binding domain of Class II aaRS
(33)
Protein domain
:
Prolyl-tRNA synthetase (ProRS) domain
(9)
Thermus thermophilus [TaxId: 274]
(4)
3a
d1hc7a1
A:277-403
3b
d1hc7b1
B:277-403
3c
d1hc7c1
C:277-403
3d
d1hc7d1
D:277-403
[
close SCOP info
]
CATH Domains
(3, 12)
Info
all CATH domains
1a: CATH_1hc7A01 (A:5-282)
1b: CATH_1hc7B01 (B:5-282)
1c: CATH_1hc7C01 (C:5-282)
1d: CATH_1hc7D01 (D:5-282)
2a: CATH_1hc7B03 (B:404-476)
2b: CATH_1hc7C03 (C:404-476)
2c: CATH_1hc7D03 (D:404-476)
2d: CATH_1hc7A03 (A:404-477)
3a: CATH_1hc7A02 (A:283-386)
3b: CATH_1hc7B02 (B:283-386)
3c: CATH_1hc7C02 (C:283-386)
3d: CATH_1hc7D02 (D:283-386)
View:
Select:
Label:
Classes
(
)
(
)
Architectures
(
)
(
)
Topologies
(
)
(
)
Homologous Superfamilies
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
2-Layer Sandwich
(8480)
Topology
:
BirA Bifunctional Protein; domain 2
(111)
Homologous Superfamily
:
Bira Bifunctional Protein; Domain 2
(111)
Thermus thermophilus. Organism_taxid: 274. Strain: hb-8.
(4)
1a
1hc7A01
A:5-282
1b
1hc7B01
B:5-282
1c
1hc7C01
C:5-282
1d
1hc7D01
D:5-282
Topology
:
Translation Initiation Factor IF3
(34)
Homologous Superfamily
:
[code=3.30.110.30, no name defined]
(9)
Thermus thermophilus. Organism_taxid: 274. Strain: hb-8.
(4)
2a
1hc7B03
B:404-476
2b
1hc7C03
C:404-476
2c
1hc7D03
D:404-476
2d
1hc7A03
A:404-477
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
[code=3.40.50.800, no name defined]
(40)
Thermus thermophilus. Organism_taxid: 274. Strain: hb-8.
(4)
3a
1hc7A02
A:283-386
3b
1hc7B02
B:283-386
3c
1hc7C02
C:283-386
3d
1hc7D02
D:283-386
[
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
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 (323 KB)
Header - Asym.Unit
Biol.Unit 1 (161 KB)
Header - Biol.Unit 1
Biol.Unit 2 (162 KB)
Header - Biol.Unit 2
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
1HC7
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
