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.
3OL9
Asym. Unit
Info
Asym.Unit (778 KB)
Biol.Unit 1 (196 KB)
Biol.Unit 2 (196 KB)
Biol.Unit 3 (196 KB)
Biol.Unit 4 (197 KB)
(using Jmol or JSmol)
spin
show selected part
auto zoom/center
Standard Views
(
Basic
|
Advanced
Interface
)
(
Basic
|
Advanced
Interface
)
Help
(1)
Title
:
POLIOVIRUS POLYMERASE ELONGATION COMPLEX WITH 3'-DEOXY-CTP
Authors
:
P. Gong, O. B. Peersen
Date
:
25 Aug 10 (Deposition) - 22 Dec 10 (Release) - 12 Jan 11 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.25
Chains
:
Asym. Unit : A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P
Biol. Unit 1: A,B,C,D (1x)
Biol. Unit 2: E,F,G,H (1x)
Biol. Unit 3: I,J,K,L (1x)
Biol. Unit 4: M,N,O,P (1x)
Keywords
:
Rna-Dependent Rna Polymerase, Elongation Complex, Virus, Protein-Rna Complex, Transferase-Rna Complex
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
P. Gong, O. B. Peersen
Structural Basis For Active Site Closure By The Poliovirus Rna-Dependent Rna Polymerase.
Proc. Natl. Acad. Sci. Usa V. 107 22505 2010
[
close entry info
]
Hetero Components
(4, 27)
Info
All Hetero Components
1a: ISOPROPYL ALCOHOL (IPAa)
1b: ISOPROPYL ALCOHOL (IPAb)
1c: ISOPROPYL ALCOHOL (IPAc)
1d: ISOPROPYL ALCOHOL (IPAd)
1e: ISOPROPYL ALCOHOL (IPAe)
1f: ISOPROPYL ALCOHOL (IPAf)
1g: ISOPROPYL ALCOHOL (IPAg)
1h: ISOPROPYL ALCOHOL (IPAh)
1i: ISOPROPYL ALCOHOL (IPAi)
1j: ISOPROPYL ALCOHOL (IPAj)
1k: ISOPROPYL ALCOHOL (IPAk)
1l: ISOPROPYL ALCOHOL (IPAl)
1m: ISOPROPYL ALCOHOL (IPAm)
1n: ISOPROPYL ALCOHOL (IPAn)
1o: ISOPROPYL ALCOHOL (IPAo)
2a: 3'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE (O2Ca)
2b: 3'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE (O2Cb)
2c: 3'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE (O2Cc)
2d: 3'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE (O2Cd)
3a: PYROPHOSPHATE 2- (POPa)
3b: PYROPHOSPHATE 2- (POPb)
3c: PYROPHOSPHATE 2- (POPc)
3d: PYROPHOSPHATE 2- (POPd)
4a: ZINC ION (ZNa)
4b: ZINC ION (ZNb)
4c: ZINC ION (ZNc)
4d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
IPA
15
Ligand/Ion
ISOPROPYL ALCOHOL
2
O2C
4
Mod. Nucleotide
3'-DEOXY-CYTIDINE-5'-MONOPHOSPHATE
3
POP
4
Ligand/Ion
PYROPHOSPHATE 2-
4
ZN
4
Ligand/Ion
ZINC ION
[
close Hetero Component info
]
Sites
(22, 22)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
ARG M:163 , ARG M:174 , HOH M:521 , O2C O:702
BINDING SITE FOR RESIDUE POP M 5001
02
AC2
SOFTWARE
ARG I:163 , ARG I:174 , HOH I:502 , HOH I:532 , O2C K:702
BINDING SITE FOR RESIDUE POP I 5002
03
AC3
SOFTWARE
ARG E:163 , LYS E:167 , ARG E:174 , HOH E:529 , HOH E:559 , O2C G:702
BINDING SITE FOR RESIDUE POP E 5003
04
AC4
SOFTWARE
ARG A:163 , LYS A:167 , ARG A:174 , HOH A:1021 , HOH C:658 , O2C C:702
BINDING SITE FOR RESIDUE POP A 5004
05
AC5
SOFTWARE
CYS M:212 , ASP M:213 , PHE M:217 , HOH M:1094
BINDING SITE FOR RESIDUE IPA M 6001
06
AC6
SOFTWARE
ASP M:183 , TYR M:264 , TYR M:267 , LEU M:268 , HOH M:807
BINDING SITE FOR RESIDUE IPA M 6004
07
AC7
SOFTWARE
GLU I:227 , LEU I:229 , VAL I:366 , THR I:367
BINDING SITE FOR RESIDUE IPA I 6006
08
AC8
SOFTWARE
GLU A:227 , LEU A:229 , VAL A:366 , TRP A:368
BINDING SITE FOR RESIDUE IPA A 6008
09
AC9
SOFTWARE
ASP A:213 , PHE A:217
BINDING SITE FOR RESIDUE IPA A 6009
10
BC1
SOFTWARE
CYS E:212 , ASP E:213 , PHE E:217 , HOH E:1165
BINDING SITE FOR RESIDUE IPA E 6010
11
BC2
SOFTWARE
ASN I:151 , ASP I:183 , MET I:187 , TYR I:264 , TYR I:267
BINDING SITE FOR RESIDUE IPA I 6011
12
BC3
SOFTWARE
ILE E:388
BINDING SITE FOR RESIDUE IPA E 6014
13
BC4
SOFTWARE
ARG M:379 , VAL M:391
BINDING SITE FOR RESIDUE IPA M 6023
14
BC5
SOFTWARE
LEU M:25 , SER M:400 , TRP M:403 , HIS M:413 , G O:698 , A O:699
BINDING SITE FOR RESIDUE IPA O 6024
15
BC6
SOFTWARE
SER I:400 , TRP I:403 , LYS I:405 , HIS I:413 , HOH I:1127 , G K:698 , A K:699
BINDING SITE FOR RESIDUE IPA I 6027
16
BC7
SOFTWARE
LEU A:25 , SER A:400 , TRP A:403 , THR A:404 , HIS A:413 , HOH A:1219 , G C:698
BINDING SITE FOR RESIDUE IPA A 6029
17
BC8
SOFTWARE
HIS E:272 , HOH E:1082 , ZN E:2002
BINDING SITE FOR RESIDUE IPA E 6030
18
BC9
SOFTWARE
TRP A:5 , HIS A:272 , HOH A:749 , ZN A:2001
BINDING SITE FOR RESIDUE IPA A 6032
19
CC1
SOFTWARE
HIS A:270 , HIS A:272 , CYS A:281 , HOH A:749 , IPA A:6032
BINDING SITE FOR RESIDUE ZN A 2001
20
CC2
SOFTWARE
HIS E:270 , HIS E:272 , CYS E:281 , HOH E:1082 , IPA E:6030
BINDING SITE FOR RESIDUE ZN E 2002
21
CC3
SOFTWARE
TRP I:5 , HIS I:270 , HIS I:272 , CYS I:281 , HOH I:560
BINDING SITE FOR RESIDUE ZN I 2003
22
CC4
SOFTWARE
TRP M:5 , HIS M:270 , HIS M:272 , CYS M:281
BINDING SITE FOR RESIDUE ZN M 2004
[
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
(1, 4)
Info
All SCOP Domains
1a: SCOP_d3ol9a_ (A:)
1b: SCOP_d3ol9e_ (E:)
1c: SCOP_d3ol9i_ (I:)
1d: SCOP_d3ol9m_ (M:)
View:
Select:
Label:
Classes
(
)
(
)
Folds
(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Multi-domain proteins (alpha and beta)
(2421)
Fold
:
DNA/RNA polymerases
(850)
Superfamily
:
DNA/RNA polymerases
(850)
Family
:
RNA-dependent RNA-polymerase
(253)
Protein domain
:
Viral RNA polymerase
(148)
Poliovirus type 1, strain Mahoney [TaxId: 12080]
(12)
1a
d3ol9a_
A:
1b
d3ol9e_
E:
1c
d3ol9i_
I:
1d
d3ol9m_
M:
[
close SCOP info
]
CATH Domains
(0, 0)
Info
all CATH domains
View:
Select:
Label:
Sorry, no Info available
[
close CATH info
]
Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_RdRP_1_3ol9M01 (M:17-460)
1b: PFAM_RdRP_1_3ol9M02 (M:17-460)
1c: PFAM_RdRP_1_3ol9M03 (M:17-460)
1d: PFAM_RdRP_1_3ol9M04 (M:17-460)
View:
Select:
Label:
Clans
(
)
(
)
Families
(
)
(
)
Organisms
(
)
(
)
Clan
:
RdRP
(210)
Family
:
RdRP_1
(44)
Human poliovirus 1
(6)
1a
RdRP_1-3ol9M01
M:17-460
1b
RdRP_1-3ol9M02
M:17-460
1c
RdRP_1-3ol9M03
M:17-460
1d
RdRP_1-3ol9M04
M:17-460
[
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
Chain C
Chain D
Chain E
Chain F
Chain G
Chain H
Chain I
Chain J
Chain K
Chain L
Chain M
Chain N
Chain O
Chain P
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 (778 KB)
Header - Asym.Unit
Biol.Unit 1 (196 KB)
Header - Biol.Unit 1
Biol.Unit 2 (196 KB)
Header - Biol.Unit 2
Biol.Unit 3 (196 KB)
Header - Biol.Unit 3
Biol.Unit 4 (197 KB)
Header - Biol.Unit 4
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
3OL9
Jmol Script Commands
|
Jmol Color Schemes
|
Jmol Mouse Manual
|
Jmol Wiki
controls:
collapse
expand
Home
JenaLib
Jmol Scripting
Contact
Help
