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.
4DWQ
Biol. Unit 1
Info
Asym.Unit (173 KB)
Biol.Unit 1 (86 KB)
Biol.Unit 2 (86 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
RNA LIGASE RTCB-GMP/MN(2+) COMPLEX
Authors
:
C. Okada, S. Xia, M. Englert, M. Yao, D. Soll, J. Wang
Date
:
26 Feb 12 (Deposition) - 05 Sep 12 (Release) - 15 Jan 14 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B
Biol. Unit 1: A (1x)
Biol. Unit 2: B (1x)
Keywords
:
Rtcb, Guanylylation, Rna Ligase, Rtcb-Gmp, Mn2+, Ligase
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
M. Englert, S. Xia, C. Okada, A. Nakamura, V. Tanavde, M. Yao, S. H. Eom, W. H. Konigsberg, D. Soll, J. Wang
Structural And Mechanistic Insights Into Guanylylation Of Rna-Splicing Ligase Rtcb Joining Rna Between 3'-Terminal Phosphate And 5'-Oh.
Proc. Natl. Acad. Sci. Usa V. 109 15235 2012
[
close entry info
]
Hetero Components
(5, 8)
Info
All Hetero Components
1a: GUANOSINE-5'-MONOPHOSPHATE (5GPa)
1b: GUANOSINE-5'-MONOPHOSPHATE (5GPb)
2a: GLYCEROL (GOLa)
2b: GLYCEROL (GOLb)
3a: MALONATE ION (MLIa)
3b: MALONATE ION (MLIb)
3c: MALONATE ION (MLIc)
4a: MANGANESE (II) ION (MNa)
4b: MANGANESE (II) ION (MNb)
5a: PHOSPHATE ION (PO4a)
5b: PHOSPHATE ION (PO4b)
5c: PHOSPHATE ION (PO4c)
5d: PHOSPHATE ION (PO4d)
5e: PHOSPHATE ION (PO4e)
6a: PYROPHOSPHATE 2- (POPa)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
5GP
1
Ligand/Ion
GUANOSINE-5'-MONOPHOSPHATE
2
GOL
1
Ligand/Ion
GLYCEROL
3
MLI
2
Ligand/Ion
MALONATE ION
4
MN
-1
Ligand/Ion
MANGANESE (II) ION
5
PO4
3
Ligand/Ion
PHOSPHATE ION
6
POP
1
Ligand/Ion
PYROPHOSPHATE 2-
[
close Hetero Component info
]
Sites
(12, 12)
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: BC4 (SOFTWARE)
11: BC5 (SOFTWARE)
12: BC6 (SOFTWARE)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ASN A:202 , PHE A:204 , GLU A:206 , HIS A:234 , HIS A:329 , PRO A:378 , GLY A:379 , SER A:380 , MET A:381 , SER A:385 , HIS A:404 , ALA A:406 , GLY A:407 , GLU A:446 , TYR A:451 , LYS A:480 , MN A:502 , POP A:509 , HOH A:698 , HOH A:764
BINDING SITE FOR RESIDUE 5GP A 501
02
AC2
SOFTWARE
CYS A:98 , HIS A:234 , HIS A:329 , 5GP A:501 , HOH A:807
BINDING SITE FOR RESIDUE MN A 502
03
AC3
SOFTWARE
TYR A:70 , GLY A:93 , TYR A:94 , ASP A:95 , ASN A:330 , LYS A:351
BINDING SITE FOR RESIDUE MLI A 503
04
AC4
SOFTWARE
LYS A:58 , GLU A:338 , MET A:395 , LYS A:396 , GLU A:397 , THR A:398 , PHE A:399 , HOH A:830
BINDING SITE FOR RESIDUE MLI A 504
05
AC5
SOFTWARE
ASN A:106 , GLU A:111 , GLN A:313 , ASP A:318 , LEU A:319 , ARG B:7 , TRP B:13 , GLU B:32 , LYS B:39
BINDING SITE FOR RESIDUE GOL A 505
06
AC6
SOFTWARE
ARG A:190 , GLN A:194 , GLY A:239 , HOH A:706 , HOH A:767 , SER B:439 , MET B:440
BINDING SITE FOR RESIDUE PO4 A 506
07
AC7
SOFTWARE
GLU A:181 , ALA A:182 , SER A:184 , ARG A:280
BINDING SITE FOR RESIDUE PO4 A 507
08
AC8
SOFTWARE
TRP A:162 , GLU A:163 , ARG A:164 , GLU A:316
BINDING SITE FOR RESIDUE PO4 A 508
09
AC9
SOFTWARE
HIS A:67 , ASN A:202 , ARG A:408 , ARG A:412 , TYR A:451 , 5GP A:501
BINDING SITE FOR RESIDUE POP A 509
10
BC4
SOFTWARE
LYS A:125 , ARG A:436 , GLN B:134 , GLN B:189 , ARG B:190 , GLN B:194 , PO4 B:506 , HOH B:637
BINDING SITE FOR RESIDUE GOL B 504
11
BC5
SOFTWARE
LYS A:6 , ARG B:104 , ARG B:168 , ALA B:221 , TYR B:222 , TYR B:368
BINDING SITE FOR RESIDUE PO4 B 505
12
BC6
SOFTWARE
ALA A:438 , GLY B:132 , ARG B:190 , GLN B:194 , ARG B:238 , GLY B:239 , GOL B:504
BINDING SITE FOR RESIDUE PO4 B 506
[
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
(1, 1)
Info
All PROSITE Patterns/Profiles
1: INTEIN_C_TER (A:98-98)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
INTEIN_C_TER
PS50818
Intein C-terminal splicing motif profile.
RTCB_PYRHO
465-488
1
A:98-98
-
[
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, 2)
Info
All SCOP Domains
1a: SCOP_d4dwqa_ (A:)
1b: SCOP_d4dwqb_ (B:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a+b)
(23004)
Fold
:
Hypothetical protein PH1602
(7)
Superfamily
:
Hypothetical protein PH1602
(7)
Family
:
Hypothetical protein PH1602
(6)
Protein domain
:
Hypothetical protein PH1602
(5)
Pyrococcus horikoshii [TaxId: 53953]
(5)
1a
d4dwqa_
A:
1b
d4dwqb_
B:
[
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 (173 KB)
Header - Asym.Unit
Biol.Unit 1 (86 KB)
Header - Biol.Unit 1
Biol.Unit 2 (86 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
4DWQ
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
