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3OL7
Biol. Unit 3
Info
Asym.Unit (776 KB)
Biol.Unit 1 (195 KB)
Biol.Unit 2 (195 KB)
Biol.Unit 3 (196 KB)
Biol.Unit 4 (197 KB)
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(1)
Title
:
POLIOVIRUS POLYMERASE ELONGATION COMPLEX WITH CTP
Authors
:
P. Gong, O. B. Peersen
Date
:
25 Aug 10 (Deposition) - 22 Dec 10 (Release) - 05 Sep 12 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.70
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
[
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Hetero Components
(4, 9)
Info
All Hetero Components
1a: GLYCEROL (GOLa)
1b: GLYCEROL (GOLb)
1c: GLYCEROL (GOLc)
1d: GLYCEROL (GOLd)
1e: GLYCEROL (GOLe)
1f: GLYCEROL (GOLf)
1g: GLYCEROL (GOLg)
1h: GLYCEROL (GOLh)
2a: ISOPROPYL ALCOHOL (IPAa)
2b: ISOPROPYL ALCOHOL (IPAb)
2c: ISOPROPYL ALCOHOL (IPAc)
2d: ISOPROPYL ALCOHOL (IPAd)
2e: ISOPROPYL ALCOHOL (IPAe)
2f: ISOPROPYL ALCOHOL (IPAf)
2g: ISOPROPYL ALCOHOL (IPAg)
2h: ISOPROPYL ALCOHOL (IPAh)
2i: ISOPROPYL ALCOHOL (IPAi)
2j: ISOPROPYL ALCOHOL (IPAj)
2k: ISOPROPYL ALCOHOL (IPAk)
2l: ISOPROPYL ALCOHOL (IPAl)
2m: ISOPROPYL ALCOHOL (IPAm)
2n: ISOPROPYL ALCOHOL (IPAn)
2o: ISOPROPYL ALCOHOL (IPAo)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
3c: MAGNESIUM ION (MGc)
3d: MAGNESIUM ION (MGd)
3e: MAGNESIUM ION (MGe)
3f: MAGNESIUM ION (MGf)
4a: DI(HYDROXYETHYL)ETHER (PEGa)
4b: DI(HYDROXYETHYL)ETHER (PEGb)
4c: DI(HYDROXYETHYL)ETHER (PEGc)
4d: DI(HYDROXYETHYL)ETHER (PEGd)
5a: PYROPHOSPHATE 2- (POPa)
5b: PYROPHOSPHATE 2- (POPb)
5c: PYROPHOSPHATE 2- (POPc)
5d: PYROPHOSPHATE 2- (POPd)
6a: ZINC ION (ZNa)
6b: ZINC ION (ZNb)
6c: ZINC ION (ZNc)
6d: ZINC ION (ZNd)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
GOL
5
Ligand/Ion
GLYCEROL
2
IPA
2
Ligand/Ion
ISOPROPYL ALCOHOL
3
MG
-1
Ligand/Ion
MAGNESIUM ION
4
PEG
1
Ligand/Ion
DI(HYDROXYETHYL)ETHER
5
POP
1
Ligand/Ion
PYROPHOSPHATE 2-
6
ZN
-1
Ligand/Ion
ZINC ION
[
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Sites
(11, 11)
Info
All Sites
01: CC1 (SOFTWARE)
02: CC2 (SOFTWARE)
03: CC3 (SOFTWARE)
04: CC4 (SOFTWARE)
05: CC5 (SOFTWARE)
06: CC6 (SOFTWARE)
07: CC7 (SOFTWARE)
08: CC8 (SOFTWARE)
09: CC9 (SOFTWARE)
10: DC1 (SOFTWARE)
11: DC2 (SOFTWARE)
View:
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Label:
No.
Name
Evidence
Residues
Description
01
CC1
SOFTWARE
ASP I:233 , TYR I:234 , ASP I:328 , C K:702 , POP K:5002
BINDING SITE FOR RESIDUE MG I 3004
02
CC2
SOFTWARE
GLU E:69 , ASP E:71 , ARG I:7
BINDING SITE FOR RESIDUE IPA I 6012
03
CC3
SOFTWARE
LYS E:66 , ARG I:7 , GLU I:11
BINDING SITE FOR RESIDUE IPA I 6023
04
CC4
SOFTWARE
ASN I:151 , LEU I:152 , PRO I:153 , LEU I:154 , HIS I:270 , SER I:271 , HIS I:272 , HOH I:613
BINDING SITE FOR RESIDUE GOL I 8002
05
CC5
SOFTWARE
LYS I:228 , LEU I:229 , GLU I:337 , VAL I:338 , THR I:365 , VAL I:366 , GOL I:8004
BINDING SITE FOR RESIDUE GOL I 8003
06
CC6
SOFTWARE
ALA I:231 , ASP I:339 , ALA I:340 , PHE I:363 , GLU I:364 , VAL I:366 , HOH I:612 , GOL I:8003
BINDING SITE FOR RESIDUE GOL I 8004
07
CC7
SOFTWARE
SER I:28 , ALA I:29 , PHE I:30 , THR I:404 , PRO I:407 , THR I:410 , HIS I:413 , HOH I:523 , HOH I:541 , HOH I:614
BINDING SITE FOR RESIDUE GOL I 8006
08
CC8
SOFTWARE
TRP I:5 , HIS I:270 , HIS I:272 , CYS I:281 , HOH I:504
BINDING SITE FOR RESIDUE ZN I 2003
09
CC9
SOFTWARE
U J:605 , C J:606
BINDING SITE FOR RESIDUE PEG J 7003
10
DC1
SOFTWARE
CYS I:212 , TYR I:326 , U J:603 , C J:604 , HOH K:211 , G K:700
BINDING SITE FOR RESIDUE GOL J 8005
11
DC2
SOFTWARE
ARG I:163 , ARG I:174 , GLY I:236 , TYR I:237 , MG I:3004 , HOH K:358 , C K:702
BINDING SITE FOR RESIDUE POP K 5002
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SAPs(SNPs)/Variants
(0, 0)
Info
(mutated residues are only available for the asymmetric unit)
All SNPs/Variants
View:
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Sorry, no Info available
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PROSITE Patterns/Profiles
(1, 1)
Info
All PROSITE Patterns/Profiles
1: RDRP_SSRNA_POS (I:227-342)
;
View:
Select:
Label:
End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
RDRP_SSRNA_POS
PS50507
RdRp of positive ssRNA viruses catalytic domain profile.
POLG_POL1M
1975-2090
1
-
-
I:227-342
-
[
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Exons
(0, 0)
Info
All Exons
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All Exon Boundaries
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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_d3ol7a_ (A:)
1b: SCOP_d3ol7e_ (E:)
1c: SCOP_d3ol7i_ (I:)
1d: SCOP_d3ol7m_ (M:)
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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
d3ol7a_
A:
1b
d3ol7e_
E:
1c
d3ol7i_
I:
1d
d3ol7m_
M:
[
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CATH Domains
(0, 0)
Info
all CATH domains
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Sorry, no Info available
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Pfam Domains
(1, 4)
Info
all PFAM domains
1a: PFAM_RdRP_1_3ol7M01 (M:17-460)
1b: PFAM_RdRP_1_3ol7M02 (M:17-460)
1c: PFAM_RdRP_1_3ol7M03 (M:17-460)
1d: PFAM_RdRP_1_3ol7M04 (M:17-460)
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Clans
(
)
(
)
Families
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)
(
)
Organisms
(
)
(
)
Clan
:
RdRP
(210)
Family
:
RdRP_1
(44)
Human poliovirus 1
(6)
1a
RdRP_1-3ol7M01
M:17-460
1b
RdRP_1-3ol7M02
M:17-460
1c
RdRP_1-3ol7M03
M:17-460
1d
RdRP_1-3ol7M04
M:17-460
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Asymmetric Unit 1
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select chains 'A' and 'C'
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select all 'ALA' residues (Alanines) in chain 'A'
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select residue range 5 to 10 in all chains
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select residue range 5 to 10 in chain 'A'
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select non-helix/non-sheet protein parts
set fontsize 20
set label size to 20 (allowed range: 1-58)
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show SS bonds with a radius of 100 units (=0.4Å)
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Show PDB file:
Asym.Unit (776 KB)
Header - Asym.Unit
Biol.Unit 1 (195 KB)
Header - Biol.Unit 1
Biol.Unit 2 (195 KB)
Header - Biol.Unit 2
Biol.Unit 3 (196 KB)
Header - Biol.Unit 3
Biol.Unit 4 (197 KB)
Header - Biol.Unit 4
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