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.
3OXD
Biol. Unit 3
Info
Asym.Unit (168 KB)
Biol.Unit 1 (83 KB)
Biol.Unit 2 (80 KB)
Biol.Unit 3 (161 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 GLYCINE RIBOSWITCH WITH TWO MUTATIONS
Authors
:
L. Huang, A. Serganov, D. J. Patel
Date
:
21 Sep 10 (Deposition) - 29 Dec 10 (Release) - 29 Dec 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
3.00
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Biol. Unit 3: A,B (1x)
Keywords
:
Gene Expression Regulator, Glycine Riboswitch, Rna
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. Huang, A. Serganov, D. J. Patel
Structural Insights Into Ligand Recognition By A Sensing Domain Of The Cooperative Glycine Riboswitch.
Mol. Cell V. 40 774 2010
[
close entry info
]
Hetero Components
(2, 3)
Info
All Hetero Components
1a: CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC... (CCCa)
1b: CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC... (CCCb)
2a: GUANOSINE-5'-DIPHOSPHATE (GDPa)
3a: MAGNESIUM ION (MGa)
3aa: MAGNESIUM ION (MGaa)
3ab: MAGNESIUM ION (MGab)
3ac: MAGNESIUM ION (MGac)
3ad: MAGNESIUM ION (MGad)
3ae: MAGNESIUM ION (MGae)
3af: MAGNESIUM ION (MGaf)
3ag: MAGNESIUM ION (MGag)
3ah: MAGNESIUM ION (MGah)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
3g: MAGNESIUM ION (MGg)
3h: MAGNESIUM ION (MGh)
3i: MAGNESIUM ION (MGi)
3j: MAGNESIUM ION (MGj)
3k: MAGNESIUM ION (MGk)
3l: MAGNESIUM ION (MGl)
3m: MAGNESIUM ION (MGm)
3n: MAGNESIUM ION (MGn)
3o: MAGNESIUM ION (MGo)
3p: MAGNESIUM ION (MGp)
3q: MAGNESIUM ION (MGq)
3r: MAGNESIUM ION (MGr)
3s: MAGNESIUM ION (MGs)
3t: MAGNESIUM ION (MGt)
3u: MAGNESIUM ION (MGu)
3v: MAGNESIUM ION (MGv)
3w: MAGNESIUM ION (MGw)
3x: MAGNESIUM ION (MGx)
3y: MAGNESIUM ION (MGy)
3z: MAGNESIUM ION (MGz)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
CCC
2
Mod. Nucleotide
CYTIDINE-5'-PHOSPHATE-2',3'-CYCLIC PHOSPHATE
2
GDP
1
Mod. Nucleotide
GUANOSINE-5'-DIPHOSPHATE
3
MG
-1
Ligand/Ion
MAGNESIUM ION
[
close Hetero Component info
]
Sites
(30, 30)
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)
19: CC1 (SOFTWARE)
20: CC2 (SOFTWARE)
21: CC3 (SOFTWARE)
22: CC4 (SOFTWARE)
23: CC5 (SOFTWARE)
24: CC6 (SOFTWARE)
25: CC7 (SOFTWARE)
26: CC8 (SOFTWARE)
27: CC9 (SOFTWARE)
28: DC1 (SOFTWARE)
29: DC2 (SOFTWARE)
30: DC3 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
HOH A:138 , HOH A:139 , HOH A:140 , HOH A:141 , HOH A:142 , HOH A:143
BINDING SITE FOR RESIDUE MG A 101
02
AC2
SOFTWARE
HOH A:146 , HOH A:147 , HOH A:148 , HOH A:149 , HOH A:150 , HOH A:151
BINDING SITE FOR RESIDUE MG A 109
03
AC3
SOFTWARE
A A:21 , HOH A:152 , HOH A:153 , HOH A:154 , HOH A:155 , HOH A:156
BINDING SITE FOR RESIDUE MG A 110
04
AC4
SOFTWARE
HOH A:157 , HOH A:158 , HOH A:159 , HOH A:160 , HOH A:161 , HOH A:162
BINDING SITE FOR RESIDUE MG A 111
05
AC5
SOFTWARE
U A:19 , U A:20 , HOH A:163 , HOH A:164 , HOH A:165 , HOH A:166 , HOH A:167
BINDING SITE FOR RESIDUE MG A 112
06
AC6
SOFTWARE
G A:50 , HOH A:168 , HOH A:169 , HOH A:170 , HOH A:171 , HOH A:172
BINDING SITE FOR RESIDUE MG A 130
07
AC7
SOFTWARE
A A:22 , A A:75
BINDING SITE FOR RESIDUE MG A 103
08
AC8
SOFTWARE
A A:75 , A A:76
BINDING SITE FOR RESIDUE MG A 104
09
AC9
SOFTWARE
G A:10
BINDING SITE FOR RESIDUE MG A 117
10
BC1
SOFTWARE
G A:62
BINDING SITE FOR RESIDUE MG A 118
11
BC2
SOFTWARE
A A:33 , C A:66 , U A:67
BINDING SITE FOR RESIDUE MG A 120
12
BC3
SOFTWARE
G A:8 , G A:80
BINDING SITE FOR RESIDUE MG A 123
13
BC4
SOFTWARE
A A:78 , G A:79 , G A:80
BINDING SITE FOR RESIDUE MG A 124
14
BC5
SOFTWARE
G A:17 , U A:19
BINDING SITE FOR RESIDUE MG A 125
15
BC6
SOFTWARE
A A:41
BINDING SITE FOR RESIDUE MG A 126
16
BC7
SOFTWARE
A A:81
BINDING SITE FOR RESIDUE MG A 137
17
BC8
SOFTWARE
HOH A:144 , HOH A:145 , HOH B:137 , HOH B:138 , HOH B:139 , HOH B:140
BINDING SITE FOR RESIDUE MG B 106
18
BC9
SOFTWARE
C B:39 , G B:62 , HOH B:141 , HOH B:142 , HOH B:143 , HOH B:144 , HOH B:145
BINDING SITE FOR RESIDUE MG B 113
19
CC1
SOFTWARE
C B:74 , A B:75 , A B:76 , HOH B:146 , HOH B:147 , HOH B:148
BINDING SITE FOR RESIDUE MG B 114
20
CC2
SOFTWARE
HOH B:149 , HOH B:150 , HOH B:151 , HOH B:152 , HOH B:153 , HOH B:154
BINDING SITE FOR RESIDUE MG B 131
21
CC3
SOFTWARE
C B:66 , U B:67 , HOH B:155 , HOH B:156 , HOH B:157 , HOH B:158 , HOH B:159 , HOH B:160
BINDING SITE FOR RESIDUE MG B 132
22
CC4
SOFTWARE
A B:34 , HOH B:161 , HOH B:162 , HOH B:163 , HOH B:164 , HOH B:165 , HOH B:166
BINDING SITE FOR RESIDUE MG B 133
23
CC5
SOFTWARE
U B:18 , U B:20
BINDING SITE FOR RESIDUE MG B 115
24
CC6
SOFTWARE
A B:78
BINDING SITE FOR RESIDUE MG B 116
25
CC7
SOFTWARE
A B:52
BINDING SITE FOR RESIDUE MG B 119
26
CC8
SOFTWARE
A B:81
BINDING SITE FOR RESIDUE MG B 121
27
CC9
SOFTWARE
G B:17 , U B:20 , A B:21
BINDING SITE FOR RESIDUE MG B 128
28
DC1
SOFTWARE
G B:70 , A B:71
BINDING SITE FOR RESIDUE MG B 129
29
DC2
SOFTWARE
A B:75
BINDING SITE FOR RESIDUE MG B 134
30
DC3
SOFTWARE
U A:20
BINDING SITE FOR RESIDUE MG B 135
[
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
(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 (168 KB)
Header - Asym.Unit
Biol.Unit 1 (83 KB)
Header - Biol.Unit 1
Biol.Unit 2 (80 KB)
Header - Biol.Unit 2
Biol.Unit 3 (161 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
3OXD
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
