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.
4P9R
Asym. Unit
Info
Asym.Unit (87 KB)
Biol.Unit 1 (83 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
SPECIATION OF A GROUP I INTRON INTO A LARIAT CAPPING RIBOZYME (HEAVY ATOM DERIVATIVE)
Authors
:
M. Meyer, H. Nielsen, V. Olieric, P. Roblin, S. D. Johansen, E. Westhof, B. Masquida
Date
:
04 Apr 14 (Deposition) - 28 May 14 (Release) - 07 Jan 15 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
Chains
:
Asym. Unit : A
Biol. Unit 1: A (1x)
Keywords
:
Catalytic Rna, Lariat-Capping Ribozyme, Branching Reaction, Lariat Fold, Rna
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Meyer, H. Nielsen, V. Olieric, P. Roblin, S. D. Johansen, E. Westhof B. Masquida
Speciation Of A Group I Intron Into A Lariat Capping Ribozyme.
Proc. Natl. Acad. Sci. Usa V. 111 7659 2014
[
close entry info
]
Hetero Components
(2, 13)
Info
All Hetero Components
1a: IRIDIUM HEXAMMINE ION (IRIa)
1b: IRIDIUM HEXAMMINE ION (IRIb)
1c: IRIDIUM HEXAMMINE ION (IRIc)
1d: IRIDIUM HEXAMMINE ION (IRId)
1e: IRIDIUM HEXAMMINE ION (IRIe)
1f: IRIDIUM HEXAMMINE ION (IRIf)
1g: IRIDIUM HEXAMMINE ION (IRIg)
1h: IRIDIUM HEXAMMINE ION (IRIh)
1i: IRIDIUM HEXAMMINE ION (IRIi)
1j: IRIDIUM HEXAMMINE ION (IRIj)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IRI
10
Ligand/Ion
IRIDIUM HEXAMMINE ION
2
MG
3
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(13, 13)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
G A:233 , U A:234 , U A:255 , G A:256 , C A:257 , HOH A:711 , HOH A:719
binding site for residue IRI A 601
02
AC2
SOFTWARE
G A:262 , G A:263 , G A:264 , A A:553 , U A:554
binding site for residue IRI A 602
03
AC3
SOFTWARE
G A:253 , A A:254 , C A:567 , G A:568 , A A:569 , A A:570
binding site for residue IRI A 603
04
AC4
SOFTWARE
G A:281 , U A:282 , A A:335 , C A:336 , G A:337 , G A:338 , C A:339
binding site for residue IRI A 604
05
AC5
SOFTWARE
G A:228 , G A:229 , G A:230
binding site for residue IRI A 605
06
AC6
SOFTWARE
U A:239 , G A:240 , G A:241
binding site for residue IRI A 606
07
AC7
SOFTWARE
C A:5 , G A:323 , C A:324 , G A:325 , A A:326 , A A:557
binding site for residue IRI A 607
08
AC8
SOFTWARE
U A:342 , G A:343 , G A:543 , G A:544 , U A:545
binding site for residue IRI A 608
09
AC9
SOFTWARE
G A:568 , A A:571 , G A:572 , G A:573
binding site for residue IRI A 609
10
AD1
SOFTWARE
G A:294 , G A:295 , G A:296 , C A:298 , A A:300
binding site for residue IRI A 610
11
AD2
SOFTWARE
G A:325 , HOH A:727 , HOH A:728 , HOH A:729 , HOH A:730 , HOH A:731
binding site for residue MG A 611
12
AD3
SOFTWARE
HOH A:732 , HOH A:733 , HOH A:734 , HOH A:735 , HOH A:736 , HOH A:737
binding site for residue MG A 612
13
AD4
SOFTWARE
HOH A:702 , HOH A:707 , HOH A:708 , HOH A:709 , HOH A:710 , HOH A:738
binding site for residue MG A 613
[
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
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 (87 KB)
Header - Asym.Unit
Biol.Unit 1 (83 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
4P9R
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
