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1SVM
Asym. Unit
Info
Asym.Unit (382 KB)
Biol.Unit 1 (375 KB)
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(1)
Title
:
CO-CRYSTAL STRUCTURE OF SV40 LARGE T ANTIGEN HELICASE DOMAIN AND ATP
Authors
:
D. Gai, R. Zhao, C. V. Finkielstein, X. S. Chen
Date
:
29 Mar 04 (Deposition) - 19 Oct 04 (Release) - 24 Feb 09 (Revision)
Method
:
X-RAY DIFFRACTION
Resolution
:
1.94
Chains
:
Asym. Unit : A,B,C,D,E,F
Biol. Unit 1: A,B,C,D,E,F (1x)
Keywords
:
Aaa+ Fold, Viral Protein
(Keyword Search:
[
Gene Ontology, PubMed, Web (Google)
]
)
Reference
:
D. Gai, R. Zhao, D. Li, C. V. Finkielstein, X. S. Chen
Mechanisms Of Conformational Change For A Replicative Hexameric Helicase Of Sv40 Large Tumor Antigen.
Cell(Cambridge, Mass. ) V. 119 47 2004
(for further references see the
PDB file header
)
[
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]
Hetero Components
(3, 18)
Info
All Hetero Components
1a: ADENOSINE-5'-TRIPHOSPHATE (ATPa)
1b: ADENOSINE-5'-TRIPHOSPHATE (ATPb)
1c: ADENOSINE-5'-TRIPHOSPHATE (ATPc)
1d: ADENOSINE-5'-TRIPHOSPHATE (ATPd)
1e: ADENOSINE-5'-TRIPHOSPHATE (ATPe)
1f: ADENOSINE-5'-TRIPHOSPHATE (ATPf)
2a: MAGNESIUM ION (MGa)
2b: MAGNESIUM ION (MGb)
2c: MAGNESIUM ION (MGc)
2d: MAGNESIUM ION (MGd)
2e: MAGNESIUM ION (MGe)
2f: MAGNESIUM ION (MGf)
3a: ZINC ION (ZNa)
3b: ZINC ION (ZNb)
3c: ZINC ION (ZNc)
3d: ZINC ION (ZNd)
3e: ZINC ION (ZNe)
3f: ZINC ION (ZNf)
View:
Select:
Label:
No.
Name
Count
Type
Full Name
1
ATP
6
Ligand/Ion
ADENOSINE-5'-TRIPHOSPHATE
2
MG
6
Ligand/Ion
MAGNESIUM ION
3
ZN
6
Ligand/Ion
ZINC ION
[
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Sites
(18, 18)
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)
View:
Select:
Label:
No.
Name
Evidence
Residues
Description
01
AC1
SOFTWARE
CYS A:302 , CYS A:305 , HIS A:313 , HIS A:317
BINDING SITE FOR RESIDUE ZN A 700
02
AC2
SOFTWARE
CYS B:302 , CYS B:305 , HIS B:313 , HIS B:317
BINDING SITE FOR RESIDUE ZN B 700
03
AC3
SOFTWARE
CYS C:302 , CYS C:305 , HIS C:313 , HIS C:317
BINDING SITE FOR RESIDUE ZN C 700
04
AC4
SOFTWARE
CYS D:302 , CYS D:305 , HIS D:313 , HIS D:317
BINDING SITE FOR RESIDUE ZN D 700
05
AC5
SOFTWARE
CYS E:302 , CYS E:305 , HIS E:313 , HIS E:317
BINDING SITE FOR RESIDUE ZN E 700
06
AC6
SOFTWARE
CYS F:302 , CYS F:305 , HIS F:313 , HIS F:317
BINDING SITE FOR RESIDUE ZN F 700
07
AC7
SOFTWARE
THR A:433 , GLU A:473 , ATP A:800 , HOH A:802 , HOH A:935 , HOH A:936
BINDING SITE FOR RESIDUE MG A 750
08
AC8
SOFTWARE
THR B:433 , ATP B:800 , HOH B:937 , HOH B:938 , HOH B:939
BINDING SITE FOR RESIDUE MG B 750
09
AC9
SOFTWARE
THR C:433 , ATP C:800 , HOH C:803 , HOH C:811 , HOH C:926
BINDING SITE FOR RESIDUE MG C 750
10
BC1
SOFTWARE
THR D:433 , ATP D:800 , HOH D:801 , HOH D:921 , HOH D:922
BINDING SITE FOR RESIDUE MG D 750
11
BC2
SOFTWARE
HOH D:823 , THR E:433 , GLU E:473 , ASP E:474 , ATP E:800 , HOH E:957 , HOH E:958
BINDING SITE FOR RESIDUE MG E 750
12
BC3
SOFTWARE
THR F:433 , ATP F:800 , HOH F:805 , HOH F:808 , HOH F:922
BINDING SITE FOR RESIDUE MG F 750
13
BC4
SOFTWARE
LEU A:397 , ILE A:428 , ASP A:429 , SER A:430 , GLY A:431 , LYS A:432 , THR A:433 , THR A:434 , ASP A:474 , ASN A:529 , ARG A:548 , PRO A:549 , LYS A:550 , LEU A:553 , LEU A:557 , LEU A:564 , MG A:750 , HOH A:802 , HOH A:910 , HOH A:935 , HOH A:936 , LYS F:418 , ARG F:540 , HOH F:846 , HOH F:921
BINDING SITE FOR RESIDUE ATP A 800
14
BC5
SOFTWARE
LYS A:418 , ARG A:540 , HOH A:837 , LEU B:397 , ILE B:428 , ASP B:429 , SER B:430 , GLY B:431 , LYS B:432 , THR B:433 , THR B:434 , ASP B:474 , ASN B:529 , ARG B:548 , PRO B:549 , LYS B:550 , LEU B:553 , LEU B:557 , LEU B:564 , MG B:750 , HOH B:804 , HOH B:813 , HOH B:893 , HOH B:937 , HOH B:938 , HOH B:939 , HOH B:940
BINDING SITE FOR RESIDUE ATP B 800
15
BC6
SOFTWARE
LYS B:418 , ARG B:540 , HOH B:827 , LEU C:397 , ILE C:428 , ASP C:429 , SER C:430 , GLY C:431 , LYS C:432 , THR C:433 , THR C:434 , ASP C:474 , ASN C:529 , ARG C:548 , PRO C:549 , LYS C:550 , LEU C:553 , LEU C:557 , LEU C:564 , MG C:750 , HOH C:803 , HOH C:811 , HOH C:822 , HOH C:860 , HOH C:862 , HOH C:925
BINDING SITE FOR RESIDUE ATP C 800
16
BC7
SOFTWARE
LYS C:418 , ARG C:540 , HOH C:812 , HOH C:927 , LEU D:397 , ILE D:428 , ASP D:429 , SER D:430 , GLY D:431 , LYS D:432 , THR D:433 , THR D:434 , ASP D:474 , ASN D:529 , ARG D:548 , PRO D:549 , LYS D:550 , LEU D:553 , LEU D:557 , LEU D:564 , MG D:750 , HOH D:801 , HOH D:831 , HOH D:843 , HOH D:921
BINDING SITE FOR RESIDUE ATP D 800
17
BC8
SOFTWARE
LYS D:418 , ARG D:540 , HOH D:823 , HOH D:923 , LEU E:397 , ILE E:428 , ASP E:429 , SER E:430 , GLY E:431 , LYS E:432 , THR E:433 , THR E:434 , ASP E:474 , ASN E:529 , ARG E:548 , PRO E:549 , LYS E:550 , LEU E:553 , LEU E:557 , LEU E:564 , MG E:750 , HOH E:886 , HOH E:916 , HOH E:950 , HOH E:958 , HOH E:959
BINDING SITE FOR RESIDUE ATP E 800
18
BC9
SOFTWARE
LYS E:418 , ARG E:540 , HOH E:849 , HOH E:866 , HOH E:868 , LEU F:397 , ILE F:428 , ASP F:429 , SER F:430 , GLY F:431 , LYS F:432 , THR F:433 , THR F:434 , ASP F:474 , ASN F:529 , ARG F:548 , PRO F:549 , LYS F:550 , LEU F:553 , LEU F:557 , LEU F:564 , MG F:750 , HOH F:805 , HOH F:808 , HOH F:815 , HOH F:818
BINDING SITE FOR RESIDUE ATP F 800
[
close Site info
]
SAPs(SNPs)/Variants
(3, 18)
Info
(mutated residues are not available)
All SNPs/Variants
1: VAR_LT_SV40_001 (Y531Y, chain A/B/C/D/E/F, )
2: VAR_LT_SV40_002 (P549P, chain A/B/C/D/E/F, )
3: VAR_LT_SV40_003 (Y552P, chain A/B/C/D/E/F, )
View:
Select:
Label:
dbSNP
PDB
No.
Source
Variant ID
Variant
UniProt ID
Status
ID
Chain
Variant
1
UniProt
VAR_LT_SV40_001
*
F
531
Y
LT_SV40
---
---
A/B/C/D/E/F
Y
531
Y
2
UniProt
VAR_LT_SV40_002
*
A
549
P
LT_SV40
---
---
A/B/C/D/E/F
P
549
P
3
UniProt
VAR_LT_SV40_003
*
Y
552
P
LT_SV40
---
---
A/B/C/D/E/F
Y
552
P
* ID not provided by source
SNP/SAP Summary Statistics
(UniProtKB/Swiss-Prot)
[
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]
PROSITE Patterns/Profiles
(2, 8)
Info
All PROSITE Patterns/Profiles
1: ZF_LTAG_D1 (C:265-357,F:265-357)
2: SF3_HELICASE_1 (A:400-560,B:400-560,C:400-560,D:40...)
;
View:
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End label:
PROSITE
UniProtKB
PDB
No.
ID
AC
Description
ID
Location
Count
Location
1
ZF_LTAG_D1
PS51341
Zinc finger large T-antigen (T-ag) D1-type profile.
LT_SV40
265-357
2
C:265-357
F:265-357
2
SF3_HELICASE_1
PS51206
Superfamily 3 helicase of DNA viruses domain profile.
LT_SV40
400-560
6
A:400-560
B:400-560
C:400-560
D:400-560
E:400-560
F:400-560
[
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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.
SCOP Domains
(1, 6)
Info
All SCOP Domains
1a: SCOP_d1svma_ (A:)
1b: SCOP_d1svmb_ (B:)
1c: SCOP_d1svmc_ (C:)
1d: SCOP_d1svmd_ (D:)
1e: SCOP_d1svme_ (E:)
1f: SCOP_d1svmf_ (F:)
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(
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(
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(
)
(
)
Superfamilies
(
)
(
)
Families
(
)
(
)
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
:
Extended AAA-ATPase domain
(92)
Protein domain
:
Papillomavirus large T antigen helicase domain
(5)
Simian virus 40 [TaxId: 10633]
(5)
1a
d1svma_
A:
1b
d1svmb_
B:
1c
d1svmc_
C:
1d
d1svmd_
D:
1e
d1svme_
E:
1f
d1svmf_
F:
[
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]
CATH Domains
(2, 12)
Info
all CATH domains
1a: CATH_1svmA03 (A:397-549)
1b: CATH_1svmB03 (B:397-549)
1c: CATH_1svmC03 (C:397-549)
1d: CATH_1svmD03 (D:397-549)
1e: CATH_1svmE03 (E:397-549)
1f: CATH_1svmF03 (F:397-549)
2a: CATH_1svmA01 (A:266-355)
2b: CATH_1svmB01 (B:266-355)
2c: CATH_1svmC01 (C:266-355)
2d: CATH_1svmD01 (D:266-355)
2e: CATH_1svmE01 (E:266-355)
2f: CATH_1svmF01 (F:266-355)
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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)
Simian virus 40. Organism_taxid: 10633.
(4)
1a
1svmA03
A:397-549
1b
1svmB03
B:397-549
1c
1svmC03
C:397-549
1d
1svmD03
D:397-549
1e
1svmE03
E:397-549
1f
1svmF03
F:397-549
Class
:
Mainly Alpha
(13335)
Architecture
:
Orthogonal Bundle
(10391)
Topology
:
Arc Repressor Mutant, subunit A
(1030)
Homologous Superfamily
:
Large t antigen; domain 1
(5)
Simian virus 40. Organism_taxid: 10633.
(4)
2a
1svmA01
A:266-355
2b
1svmB01
B:266-355
2c
1svmC01
C:266-355
2d
1svmD01
D:266-355
2e
1svmE01
E:266-355
2f
1svmF01
F:266-355
[
close CATH info
]
Pfam Domains
(1, 6)
Info
all PFAM domains
1a: PFAM_Polyoma_lg_T_C_1svmF01 (F:265-627)
1b: PFAM_Polyoma_lg_T_C_1svmF02 (F:265-627)
1c: PFAM_Polyoma_lg_T_C_1svmF03 (F:265-627)
1d: PFAM_Polyoma_lg_T_C_1svmF04 (F:265-627)
1e: PFAM_Polyoma_lg_T_C_1svmF05 (F:265-627)
1f: PFAM_Polyoma_lg_T_C_1svmF06 (F:265-627)
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)
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(
)
(
)
Clan
:
P-loop_NTPase
(1112)
Family
:
Polyoma_lg_T_C
(4)
Simian virus 40 (SV40)
(4)
1a
Polyoma_lg_T_C-1svmF01
F:265-627
1b
Polyoma_lg_T_C-1svmF02
F:265-627
1c
Polyoma_lg_T_C-1svmF03
F:265-627
1d
Polyoma_lg_T_C-1svmF04
F:265-627
1e
Polyoma_lg_T_C-1svmF05
F:265-627
1f
Polyoma_lg_T_C-1svmF06
F:265-627
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