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.
2XBM
Biol. Unit 2
Info
Asym.Unit (387 KB)
Biol.Unit 1 (191 KB)
Biol.Unit 2 (191 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 THE DENGUE VIRUS METHYLTRANSFERASE BOUND TO A 5'-CAPPED OCTAMERIC RNA
Authors
:
L. J. Yap, D. H. Luo, K. Y. Chung, S. P. Lim, C. Bodenreider, C. Noble, P. Y. J. Lescar
Date
:
13 Apr 10 (Deposition) - 29 Sep 10 (Release) - 04 Apr 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.90
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: B,D,E (1x)
Biol. Unit 2: A,C,F (1x)
Keywords
:
Flavivirus, Rna Binding Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
L. J. Yap, D. H. Luo, K. Y. Chung, S. P. Lim, C. Bodenreider, C. Noble, P. Y. Shi, J. Lescar
Crystal Structure Of The Dengue Virus Methyltransferase Bound To A 5'-Capped Octameric Rna
Plos One V. 5 12836 2010
[
close entry info
]
Hetero Components
(4, 10)
Info
All Hetero Components
1a: GUANOSINE-P3-ADENOSINE-5',5'-TRIPH... (G3Aa)
1b: GUANOSINE-P3-ADENOSINE-5',5'-TRIPH... (G3Ab)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: S-ADENOSYL-L-HOMOCYSTEINE (SAHa)
3b: S-ADENOSYL-L-HOMOCYSTEINE (SAHb)
3c: S-ADENOSYL-L-HOMOCYSTEINE (SAHc)
3d: S-ADENOSYL-L-HOMOCYSTEINE (SAHd)
4a: SULFATE ION (SO4a)
4b: SULFATE ION (SO4b)
4c: SULFATE ION (SO4c)
4d: SULFATE ION (SO4d)
4e: SULFATE ION (SO4e)
4f: SULFATE ION (SO4f)
4g: SULFATE ION (SO4g)
4h: SULFATE ION (SO4h)
4i: SULFATE ION (SO4i)
4j: SULFATE ION (SO4j)
4k: SULFATE ION (SO4k)
4l: SULFATE ION (SO4l)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
G3A
1
Mod. Nucleotide
GUANOSINE-P3-ADENOSINE-5',5'-TRIPHOSPHATE
2
GOL
1
Ligand/Ion
GLYCEROL
3
SAH
2
Ligand/Ion
S-ADENOSYL-L-HOMOCYSTEINE
4
SO4
6
Ligand/Ion
SULFATE ION
[
close Hetero Component info
]
Sites
(9, 9)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
7: BC4 (SOFTWARE)
8: BC5 (SOFTWARE)
9: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ARG A:38 , LYS A:42 , ARG A:57 , ARG A:84 , HOH A:2093
BINDING SITE FOR RESIDUE SO4 A 264
2
AC2
SOFTWARE
ARG A:76 , ARG A:101
BINDING SITE FOR RESIDUE SO4 A 265
3
AC3
SOFTWARE
SER A:229 , ASN A:232 , ARG A:236 , HOH A:2094
BINDING SITE FOR RESIDUE SO4 A 266
4
AC4
SOFTWARE
LYS A:29 , LYS A:30 , ARG A:211
BINDING SITE FOR RESIDUE SO4 A 267
5
AC5
SOFTWARE
SER A:56 , GLY A:58 , GLY A:81 , CYS A:82 , GLY A:83 , GLY A:86 , TRP A:87 , THR A:104 , LYS A:105 , LYS A:130 , ASP A:131 , VAL A:132 , PHE A:133 , ASP A:146 , HOH A:2095 , HOH A:2096 , HOH A:2097
BINDING SITE FOR RESIDUE SAH A 268
6
AC6
SOFTWARE
LYS A:61
BINDING SITE FOR RESIDUE GOL A 269
7
BC4
SOFTWARE
GLY C:109 , HIS C:110 , GLU C:111 , SAH C:266 , HOH C:2117
BINDING SITE FOR RESIDUE SO4 C 264
8
BC5
SOFTWARE
ARG C:38 , LYS C:42 , ARG C:57 , ARG C:84
BINDING SITE FOR RESIDUE SO4 C 265
9
BC6
SOFTWARE
SER C:56 , GLY C:58 , GLY C:81 , CYS C:82 , GLY C:86 , TRP C:87 , LYS C:105 , LYS C:130 , ASP C:131 , VAL C:132 , PHE C:133 , ASP C:146 , SO4 C:264 , HOH C:2038 , HOH C:2047 , HOH C:2118
BINDING SITE FOR RESIDUE SAH C 266
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d2xbma_ (A:)
1b: SCOP_d2xbmb_ (B:)
1c: SCOP_d2xbmc_ (C:)
1d: SCOP_d2xbmd_ (D:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Superfamily
:
S-adenosyl-L-methionine-dependent methyltransferases
(533)
Family
:
mRNA cap methylase
(41)
Protein domain
:
automated matches
(8)
Dengue virus [TaxId: 12637]
(1)
1a
d2xbma_
A:
1b
d2xbmb_
B:
1c
d2xbmc_
C:
1d
d2xbmd_
D:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(2, 8)
Info
all PFAM domains
1a: PFAM_FtsJ_2xbmD01 (D:54-224)
1b: PFAM_FtsJ_2xbmD02 (D:54-224)
1c: PFAM_FtsJ_2xbmD03 (D:54-224)
1d: PFAM_FtsJ_2xbmD04 (D:54-224)
2a: PFAM_Flavi_NS5_2xbmD05 (D:250-263)
2b: PFAM_Flavi_NS5_2xbmD06 (D:250-263)
2c: PFAM_Flavi_NS5_2xbmD07 (D:250-263)
2d: PFAM_Flavi_NS5_2xbmD08 (D:250-263)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
NADP_Rossmann
(1239)
Family
:
FtsJ
(23)
Dengue virus 3
(3)
1a
FtsJ-2xbmD01
D:54-224
1b
FtsJ-2xbmD02
D:54-224
1c
FtsJ-2xbmD03
D:54-224
1d
FtsJ-2xbmD04
D:54-224
Clan
:
RdRP
(210)
Family
:
Flavi_NS5
(21)
Dengue virus 3
(3)
2a
Flavi_NS5-2xbmD05
D:250-263
2b
Flavi_NS5-2xbmD06
D:250-263
2c
Flavi_NS5-2xbmD07
D:250-263
2d
Flavi_NS5-2xbmD08
D:250-263
[
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 C
Chain F
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 (387 KB)
Header - Asym.Unit
Biol.Unit 1 (191 KB)
Header - Biol.Unit 1
Biol.Unit 2 (191 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
2XBM
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
