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3KQL
Asym. Unit
Info
Asym.Unit (148 KB)
Biol.Unit 1 (74 KB)
Biol.Unit 2 (74 KB)
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(1)
Title
:
THREE CONFORMATIONAL SNAPSHOTS OF THE HEPATITIS C VIRUS NS3 HELICASE REVEAL A RATCHET TRANSLOCATION MECHANISM
Authors
:
M. Gu, C. M. Rice
Date
:
17 Nov 09 (Deposition) - 26 Jan 10 (Release) - 26 Jan 10 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
2.50
Chains
:
Asym. Unit : A,B,E,F
Biol. Unit 1: A,E (1x)
Biol. Unit 2: B,F (1x)
Keywords
:
Helicase-Substrate Transition-State Complex, Hcv, Ns3 Protein, Helicase, Dna-Binding
(Keyword Search:
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Reference
:
M. Gu, C. M. Rice
Three Conformational Snapshots Of The Hepatitis C Virus Ns3 Helicase Reveal A Ratchet Translocation Mechanism.
Proc. Natl. Acad. Sci. Usa V. 107 521 2010
(for further references see the
PDB file header
)
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Hetero Components
(3, 6)
Info
All Hetero Components
1a: ADENOSINE-5'-DIPHOSPHATE (ADPa)
1b: ADENOSINE-5'-DIPHOSPHATE (ADPb)
2a: TETRAFLUOROALUMINATE ION (ALFa)
2b: TETRAFLUOROALUMINATE ION (ALFb)
3a: MAGNESIUM ION (MGa)
3b: MAGNESIUM ION (MGb)
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No.
Name
Count
Type
Full Name
1
ADP
2
Ligand/Ion
ADENOSINE-5'-DIPHOSPHATE
2
ALF
2
Ligand/Ion
TETRAFLUOROALUMINATE ION
3
MG
2
Ligand/Ion
MAGNESIUM ION
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Sites
(6, 6)
Info
All Sites
1: AC1 (SOFTWARE)
2: AC2 (SOFTWARE)
3: AC3 (SOFTWARE)
4: AC4 (SOFTWARE)
5: AC5 (SOFTWARE)
6: AC6 (SOFTWARE)
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No.
Name
Evidence
Residues
Description
1
AC1
SOFTWARE
ADP A:2 , MG A:3 , HOH A:5 , THR A:206 , GLY A:207 , LYS A:210 , GLU A:291 , GLY A:417 , ARG A:464 , ARG A:467 , HOH A:626 , HOH A:627 , HOH A:628
BINDING SITE FOR RESIDUE ALF A 1
2
AC2
SOFTWARE
ALF A:1 , MG A:3 , HOH A:4 , HOH A:6 , GLY A:207 , SER A:208 , GLY A:209 , LYS A:210 , SER A:211 , THR A:212 , TYR A:241 , THR A:419 , ARG A:467 , GLY A:468 , HOH A:628
BINDING SITE FOR RESIDUE ADP A 2
3
AC3
SOFTWARE
ALF A:1 , ADP A:2 , HOH A:4 , SER A:211 , HOH A:627 , HOH A:628
BINDING SITE FOR RESIDUE MG A 3
4
AC4
SOFTWARE
ADP B:2 , MG B:3 , HOH B:7 , HOH B:8 , HOH B:10 , HOH B:12 , THR B:206 , GLY B:207 , LYS B:210 , GLU B:291 , GLY B:417 , ARG B:464 , ARG B:467
BINDING SITE FOR RESIDUE ALF B 1
5
AC5
SOFTWARE
ALF B:1 , MG B:3 , HOH B:8 , HOH B:11 , GLY B:207 , SER B:208 , GLY B:209 , LYS B:210 , SER B:211 , THR B:212 , TYR B:241 , THR B:419 , ARG B:467 , GLY B:468
BINDING SITE FOR RESIDUE ADP B 2
6
AC6
SOFTWARE
ALF B:1 , ADP B:2 , HOH B:8 , HOH B:9 , HOH B:10 , SER B:211
BINDING SITE FOR RESIDUE MG B 3
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SAPs(SNPs)/Variants
(0, 0)
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PROSITE Patterns/Profiles
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Exons
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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_d3kqla1 (A:189-325)
1b: SCOP_d3kqlb1 (B:189-325)
1c: SCOP_d3kqlb2 (B:326-625)
1d: SCOP_d3kqla2 (A:326-625)
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)
Protein Domains
(
)
(
)
Organisms
(
)
(
)
Class
:
Alpha and beta proteins (a/b)
(23833)
Fold
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Superfamily
:
P-loop containing nucleoside triphosphate hydrolases
(2083)
Family
:
RNA helicase
(31)
Protein domain
:
HCV helicase domain
(16)
Human hepatitis C virus (HCV), different isolates [TaxId: 11103]
(16)
1a
d3kqla1
A:189-325
1b
d3kqlb1
B:189-325
1c
d3kqlb2
B:326-625
1d
d3kqla2
A:326-625
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CATH Domains
(2, 6)
Info
all CATH domains
1a: CATH_3kqlA01 (A:189-326)
1b: CATH_3kqlB01 (B:189-326)
1c: CATH_3kqlA02 (A:327-430,A:452-483)
1d: CATH_3kqlB02 (B:327-430,B:452-483)
2a: CATH_3kqlA03 (A:431-451,A:484-625)
2b: CATH_3kqlB03 (B:431-451,B:484-625)
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)
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)
(
)
Organisms
(
)
(
)
Class
:
Alpha Beta
(26913)
Architecture
:
3-Layer(aba) Sandwich
(12045)
Topology
:
Rossmann fold
(7312)
Homologous Superfamily
:
P-loop containing nucleotide triphosphate hydrolases
(1378)
Hcv (Hepatitis c virus)
(5)
1a
3kqlA01
A:189-326
1b
3kqlB01
B:189-326
1c
3kqlA02
A:327-430,A:452-483
1d
3kqlB02
B:327-430,B:452-483
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
RNA Helicase; Chain A, domain 3
(11)
Homologous Superfamily
:
RNA Helicase Chain A , domain 3
(11)
Hcv (Hepatitis c virus)
(5)
2a
3kqlA03
A:431-451,A:484-625
2b
3kqlB03
B:431-451,B:484-625
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Pfam Domains
(1, 2)
Info
all PFAM domains
1a: PFAM_Flavi_DEAD_3kqlB01 (B:255-336)
1b: PFAM_Flavi_DEAD_3kqlB02 (B:255-336)
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Clan
:
P-loop_NTPase
(1112)
Family
:
Flavi_DEAD
(27)
Hepatitis C virus genotype 1b (isolate Con1) (HCV)
(5)
1a
Flavi_DEAD-3kqlB01
B:255-336
1b
Flavi_DEAD-3kqlB02
B:255-336
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Asymmetric Unit 1
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Show PDB file:
Asym.Unit (148 KB)
Header - Asym.Unit
Biol.Unit 1 (74 KB)
Header - Biol.Unit 1
Biol.Unit 2 (74 KB)
Header - Biol.Unit 2
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