1SVM - JenaLib

Asym./Biol. Unit (Jmol Viewer)

Asym./Biol. Unit - sites (Jmol Viewer)

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./Biol. Unit : A,B,C,D,E,F

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
PubMed-ID: 15454080 | Reference-DOI: 10.1016/J.CELL.2004.09.017
(for further references see the PDB file header)

Molecule 1 - LARGE T ANTIGEN
	Chains	:	A, B, C, D, E, F
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Fragment	:	HELICASE DOMAIN
	Organism Scientific	:	SIMIAN VIRUS 40
	Organism Taxid	:	10633

		1	2	3	4	5	6
Asymmetric/Biological Unit	:	A	B	C	D	E	F

Summary Information (see also Sequences/Alignments below)

Asymmetric/Biological Unit (3, 18)

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

Asymmetric Unit (18, 18)

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

(no "SS Bond" information available for 1SVM)

(no "Cis Peptide Bond" information available for 1SVM)

Asymmetric/Biological Unit (3, 18)

								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)

Asymmetric/Biological Unit (2, 8)

	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

(no "Exon" information available for 1SVM)

Asymmetric/Biological Unit

Reformat:	Number of residues per line = ('0' or empty: single-line sequence representation)
	Number of residues per labelling interval =
	UniProt sequence: complete aligned part

Show mapping:	SCOP domains	CATH domains	Pfam domains	Secondary structure (by author)
	SAPs(SNPs)	PROSITE motifs	Exons
	(details for a mapped element are shown in a popup box when the mouse pointer rests over it)

Chain A from PDB  Type:PROTEIN  Length:362
 aligned with LT_SV40 | P03070 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:362
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625  
              LT_SV40   266 KQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEFSVPKTLQARFVKQIDFRAKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD 627
               SCOP domains d1svma_ A: Papillomavirus large T antigen helicase domain                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1svmA01 A:266-355 Large t antigen; domain 1                                               -----------------------------------------1svmA03 A:397-549 P-loop containing nucleotide triphosphate hydrolases                                                                                   ------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh.eee.......hhhhhhhhhh....eee................hhhhhhhhhhhhhhh...eee.......eee....eeeee.....hhhhhh.eeeeee...hhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-----------------P--P--------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZF_LTAG_D1  PDB: - UniProt: 265-357                                                         ------------------------------------------SF3_HELICASE_1  PDB: A:400-560 UniProt: 400-560                                                                                                                  ------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1svm A 266 KQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD 627
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625

Chain B from PDB  Type:PROTEIN  Length:362
 aligned with LT_SV40 | P03070 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:362
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625  
              LT_SV40   266 KQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEFSVPKTLQARFVKQIDFRAKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD 627
               SCOP domains d1svmb_ B: Papillomavirus large T antigen helicase domain                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1svmB01 B:266-355 Large t antigen; domain 1                                               -----------------------------------------1svmB03 B:397-549 P-loop containing nucleotide triphosphate hydrolases                                                                                   ------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh.eee....hhhhhhhhhhhhh....eee.......hhhhh....hhhhhhhhhhhhhhh...eeee.....eeee....eeeee.....hhhhhh.eeeeee...hhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh...... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-----------------P--P--------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZF_LTAG_D1  PDB: - UniProt: 265-357                                                         ------------------------------------------SF3_HELICASE_1  PDB: B:400-560 UniProt: 400-560                                                                                                                  ------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1svm B 266 KQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD 627
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625

Chain C from PDB  Type:PROTEIN  Length:363
 aligned with LT_SV40 | P03070 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:363
                                   274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624   
              LT_SV40   265 TKQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEFSVPKTLQARFVKQIDFRAKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD 627
               SCOP domains d1svmc_ C: Papillomavirus large T antigen helicase domain                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -1svmC01 C:266-355 Large t antigen; domain 1                                               -----------------------------------------1svmC03 C:397-549 P-loop containing nucleotide triphosphate hydrolases                                                                                   ------------------------------------------------------------------------------ CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ....hhhhhhhhhhhh...hhhhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhh...hhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhheeee....hhhhhhhhhhhhh...eeee................hhhhhhh.hhhhhhh...eeee....eeeee....eeeee.....hhhhhh.eeeeee...hhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-----------------P--P--------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZF_LTAG_D1  PDB: C:265-357 UniProt: 265-357                                                  ------------------------------------------SF3_HELICASE_1  PDB: C:400-560 UniProt: 400-560                                                                                                                  ------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1svm C 265 TKQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD 627
                                   274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624

Chain D from PDB  Type:PROTEIN  Length:362
 aligned with LT_SV40 | P03070 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:362
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625  
              LT_SV40   266 KQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEFSVPKTLQARFVKQIDFRAKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD 627
               SCOP domains d1svmd_ D: Papillomavirus large T antigen helicase domain                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1svmD01 D:266-355 Large t antigen; domain 1                                               -----------------------------------------1svmD03 D:397-549 P-loop containing nucleotide triphosphate hydrolases                                                                                   ------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhhhhh.hhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh.eee.......hhhhhhhh......eee.......hhhhh....hhhhhhhhhhhhhhh...eeee....eeeee....eeeee.....hhhhhh.eeeeee...hhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..hhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-----------------P--P--------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZF_LTAG_D1  PDB: - UniProt: 265-357                                                         ------------------------------------------SF3_HELICASE_1  PDB: D:400-560 UniProt: 400-560                                                                                                                  ------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1svm D 266 KQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD 627
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625

Chain E from PDB  Type:PROTEIN  Length:362
 aligned with LT_SV40 | P03070 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:362
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625  
              LT_SV40   266 KQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEFSVPKTLQARFVKQIDFRAKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD 627
               SCOP domains d1svme_ E: Papillomavirus large T antigen helicase domain                                                                                                                                                                                                                                                                                                                  SCOP domains
               CATH domains 1svmE01 E:266-355 Large t antigen; domain 1                                               -----------------------------------------1svmE03 E:397-549 P-loop containing nucleotide triphosphate hydrolases                                                                                   ------------------------------------------------------------------------------ CATH domains
               Pfam domains -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...hhhhhhhhhhhhh..hhhhhhhhhhhh......hhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhheeee.......hhhhhhhhhh...eeee.......hhhhh....hhhhhhhhhhhhhhh...eeee.....eeee....eeeee.....hhhhhh.eeeeee...hhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-----------------P--P--------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZF_LTAG_D1  PDB: - UniProt: 265-357                                                         ------------------------------------------SF3_HELICASE_1  PDB: E:400-560 UniProt: 400-560                                                                                                                  ------------------------------------------------------------------- PROSITE
                 Transcript -------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1svm E 266 KQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD 627
                                   275       285       295       305       315       325       335       345       355       365       375       385       395       405       415       425       435       445       455       465       475       485       495       505       515       525       535       545       555       565       575       585       595       605       615       625

Chain F from PDB  Type:PROTEIN  Length:363
 aligned with LT_SV40 | P03070 from UniProtKB/Swiss-Prot  Length:708

    Alignment length:363
                                   274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624   
              LT_SV40   265 TKQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEFSVPKTLQARFVKQIDFRAKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD 627
               SCOP domains d1svmf_ F: Papillomavirus large T antigen helicase domain                                                                                                                                                                                                                                                                                                                   SCOP domains
               CATH domains -1svmF01 F:266-355 Large t antigen; domain 1                                               -----------------------------------------1svmF03 F:397-549 P-loop containing nucleotide triphosphate hydrolases                                                                                   ------------------------------------------------------------------------------ CATH domains
           Pfam domains (1) Polyoma_lg_T_C-1svmF01 F:265-627                                                                                                                                                                                                                                                                                                                                            Pfam domains (1)
           Pfam domains (2) Polyoma_lg_T_C-1svmF02 F:265-627                                                                                                                                                                                                                                                                                                                                            Pfam domains (2)
           Pfam domains (3) Polyoma_lg_T_C-1svmF03 F:265-627                                                                                                                                                                                                                                                                                                                                            Pfam domains (3)
           Pfam domains (4) Polyoma_lg_T_C-1svmF04 F:265-627                                                                                                                                                                                                                                                                                                                                            Pfam domains (4)
           Pfam domains (5) Polyoma_lg_T_C-1svmF05 F:265-627                                                                                                                                                                                                                                                                                                                                            Pfam domains (5)
           Pfam domains (6) Polyoma_lg_T_C-1svmF06 F:265-627                                                                                                                                                                                                                                                                                                                                            Pfam domains (6)
         Sec.struct. author ....hhhhhhhhhhhh...hhhhhhhhhhhhhh....hhhhhh..hhhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......hhhhhhhhhhhhh....hhhhhhhhhhhhhhhh.....eeeee.....hhhhhhhhhhhhhh.eee.......hhhhhhhh......eee.......hhhhh....hhhhhhhhhhhhhhh...eee.......eee....eeeee.....hhhhhh.eeeeee...hhhhhhhhhh.hhhhhh....hhhhhhhhhhhhhhhhhh...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh..... Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------Y-----------------P--P--------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ZF_LTAG_D1  PDB: F:265-357 UniProt: 265-357                                                  ------------------------------------------SF3_HELICASE_1  PDB: F:400-560 UniProt: 400-560                                                                                                                  ------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1svm F 265 TKQVSWKLVTEYAMETKCDDVLLLLGMYLEFQYSFEMCLKCIKKEQPSHYKYHEKHYANAAIFADSKNQKTICQQAVDTVLAKKRVDSLQLTREQMLTNRFNDLLDRMDIMFGSTGSADIEEWMAGVAWLHCLLPKMDSVVYDFLKCMVYNIPKKRYWLFKGPIDSGKTTLAAALLELCGGKALNVNLPLDRLNFELGVAIDQFLVVFEDVKGTGGESRDLPSGQGINNLDNLRDYLDGSVKVNLEKKHLNKRTQIFPPGIVTMNEYSVPKTLQARFVKQIDFRPKDYLKHCLERSEFLLEKRIIQSGIALLLMLIWYRPVAEFAQSIQSRIVEWKERLDKEFSLSVYQKMKFNVAMGIGVLD 627
                                   274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434       444       454       464       474       484       494       504       514       524       534       544       554       564       574       584       594       604       614       624

Legend:		→ Mismatch	(orange background)
	-	→ Gap	(green background, '-', border residues have a numbering label)
		→ Modified Residue	(blue background, lower-case, 'x' indicates undefined single-letter code, labelled with number + name)
	x	→ Chemical Group	(purple background, 'x', labelled with number + name, e.g. ACE or NH2)
	extra numbering lines below/above indicate numbering irregularities and modified residue names etc., number ends below/above '\|'

Asymmetric/Biological Unit

Classes(

)

Folds(

)

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:

Asymmetric/Biological Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

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

Asymmetric/Biological Unit

Clans(

)

Families(

)

Organisms( (-)

)

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

Asymmetric/Biological Unit(hide GO term definitions)

Chain A,B,C,D,E,F (LT_SV40 | P03070)

molecular function
	GO:0005524	ATP binding	Interacting selectively and non-covalently with ATP, adenosine 5'-triphosphate, a universally important coenzyme and enzyme regulator.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003688	DNA replication origin binding	Interacting selectively and non-covalently with the DNA replication origin, a unique DNA sequence of a replicon at which DNA replication is initiated and proceeds bidirectionally or unidirectionally.
	GO:0003690	double-stranded DNA binding	Interacting selectively and non-covalently with double-stranded DNA.
	GO:0004386	helicase activity	Catalysis of the reaction: NTP + H2O = NDP + phosphate, to drive the unwinding of a DNA or RNA helix.
	GO:0016787	hydrolase activity	Catalysis of the hydrolysis of various bonds, e.g. C-O, C-N, C-C, phosphoric anhydride bonds, etc. Hydrolase is the systematic name for any enzyme of EC class 3.
	GO:0046872	metal ion binding	Interacting selectively and non-covalently with any metal ion.
	GO:0000166	nucleotide binding	Interacting selectively and non-covalently with a nucleotide, any compound consisting of a nucleoside that is esterified with (ortho)phosphate or an oligophosphate at any hydroxyl group on the ribose or deoxyribose.
	GO:0005515	protein binding	Interacting selectively and non-covalently with any protein or protein complex (a complex of two or more proteins that may include other nonprotein molecules).
	GO:0003697	single-stranded DNA binding	Interacting selectively and non-covalently with single-stranded DNA.
biological process
	GO:0006260	DNA replication	The cellular metabolic process in which a cell duplicates one or more molecules of DNA. DNA replication begins when specific sequences, known as origins of replication, are recognized and bound by initiation proteins, and ends when the original DNA molecule has been completely duplicated and the copies topologically separated. The unit of replication usually corresponds to the genome of the cell, an organelle, or a virus. The template for replication can either be an existing DNA molecule or RNA.
	GO:0006268	DNA unwinding involved in DNA replication	The process in which interchain hydrogen bonds between two strands of DNA are broken or 'melted', generating unpaired template strands for DNA replication.
	GO:0039686	bidirectional double-stranded viral DNA replication	A viral DNA replication process where replication occurs in both directions from the starting point. This creates two replication forks, moving in opposite directions.
	GO:0030683	evasion or tolerance by virus of host immune response	Any process, either active or passive, by which a virus avoids the effects of the host organism's immune response. The host is defined as the larger of the organisms involved in a symbiotic interaction.
	GO:0039645	modulation by virus of host G1/S transition checkpoint	Any viral process that modulates the frequency, rate or extent of the host cell G1/S transition checkpoint.
	GO:0060153	modulation by virus of host cell cycle	Any viral process that modulates the rate or extent of progression through the cell cycle.
	GO:0039648	modulation by virus of host protein ubiquitination	Any process in which a virus modulates the frequency, rate or extent of protein ubiquitination in the host organism. Ubiquitination is the process in which one or more ubiquitin groups are added to a protein.
	GO:0039649	modulation by virus of host ubiquitin-protein ligase activity	The process in which a virus effects a change in host ubiquitin-protein ligase activity. Ubiquitin-protein ligase activity catalyzes the reaction: ATP + ubiquitin + protein lysine = AMP + diphosphate + protein N-ubiquityllysine.
	GO:0006355	regulation of transcription, DNA-templated	Any process that modulates the frequency, rate or extent of cellular DNA-templated transcription.
	GO:0039576	suppression by virus of host JAK1 activity	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of host JAK1 (Janus Kinase 1) activity. In the host, binding of a ligand to a receptor triggers activation of JAK proteins, which phosphorylate tyrosine residues on the receptor creating sites for STAT proteins to bind, which are in turn phosphorylated and activated by JAK proteins. By blocking JAK1 activity, many viruses block the host signal transduction pathway.
	GO:0039503	suppression by virus of host innate immune response	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of the innate immune response of the host organism, the host's first line of defense.
	GO:0039502	suppression by virus of host type I interferon-mediated signaling pathway	Any process in which a virus stops, prevents, or reduces the frequency, rate or extent of type I interferon-mediated signaling in the host organism. Type I interferons include the interferon-alpha, beta, delta, episilon, zeta, kappa, tau, and omega gene families.
	GO:0006351	transcription, DNA-templated	The cellular synthesis of RNA on a template of DNA.
	GO:0039693	viral DNA genome replication	The replication of a viral DNA genome.
	GO:0016032	viral process	A multi-organism process in which a virus is a participant. The other participant is the host. Includes infection of a host cell, replication of the viral genome, and assembly of progeny virus particles. In some cases the viral genetic material may integrate into the host genome and only subsequently, under particular circumstances, 'complete' its life cycle.
cellular component
	GO:0042025	host cell nucleus	A membrane-bounded organelle as it is found in the host cell in which chromosomes are housed and replicated. The host is defined as the larger of the organisms involved in a symbiotic interaction.

Asymmetric/Biological Unit
	Complete Structure
		Jena3D(integrated viewing of ligand, site, SAP, PROSITE, SCOP information)
		WebMol \| AstexViewer[tm]@PDBe (Java Applets, require no local installation except for Java; loading may be slow)
		STRAP (Java WebStart application, automatic local installation, requires Java; full application with system access!)
		RasMol (require local installation)
		Molscript (VRML) (requires installation of a VRML viewer; select preferred view via VRML and generate a mono or stereo PDF format file)

	Ligands, Modified Residues, Ions
		ATP	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		ZN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]

	Sites
		AC1	[ RasMol ]	+environment [ RasMol ]
		AC2	[ RasMol ]	+environment [ RasMol ]
		AC3	[ RasMol ]	+environment [ RasMol ]
		AC4	[ RasMol ]	+environment [ RasMol ]
		AC5	[ RasMol ]	+environment [ RasMol ]
		AC6	[ RasMol ]	+environment [ RasMol ]
		AC7	[ RasMol ]	+environment [ RasMol ]
		AC8	[ RasMol ]	+environment [ RasMol ]
		AC9	[ RasMol ]	+environment [ RasMol ]
		BC1	[ RasMol ]	+environment [ RasMol ]
		BC2	[ RasMol ]	+environment [ RasMol ]
		BC3	[ RasMol ]	+environment [ RasMol ]
		BC4	[ RasMol ]	+environment [ RasMol ]
		BC5	[ RasMol ]	+environment [ RasMol ]
		BC6	[ RasMol ]	+environment [ RasMol ]
		BC7	[ RasMol ]	+environment [ RasMol ]
		BC8	[ RasMol ]	+environment [ RasMol ]
		BC9	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1svm)

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym./Biol. Unit PNG format \| Asym./Biol. Unit - sites PNG format ](automatic orientation, automatically generated)
Molscript
	protein, nucleic acid: cartoon; ligands: spacefill; active site: ball and stick [ mono PDF format \| stereo PDF format ](default orientation, automatically generated)

Access by PDB/NDB ID
	1svm
		Family and Domain Information	:	ProDom \| SYSTERS
		General Structural Information	:	GlycoscienceDB \| MMDB \| NDB \| OCA \| PDB \| PDBe \| PDBj \| PDBsum \| PDBWiki \| PQS \| PROTEOPEDIA
		Orientation in Membranes	:	OPM
		Protein Surface	:	SURFACE
		Secondary Structure	:	DSSP (structure derived) \| HSSP (homology derived)
		Structural Genomics	:	GeneCensus
		Structural Neighbours	:	CE \| VAST
		Structure Classification	:	CATH \| Dali \| SCOP
		Validation and Original Data	:	BMRB Data View \| BMRB Restraints Grid \| EDS \| PROCHECK \| RECOORD \| WHAT_CHECK

Access by UniProt ID/Accession number
	LT_SV40 \| P03070
		Comparative Protein Structure Models	:	ModBase
		Genomic Information	:	Ensembl
		Protein-protein Interaction	:	DIP
		Sequence, Family and Domain Information	:	InterPro \| Pfam \| SMART \| UniProtKB/SwissProt

Access by Enzyme Classificator (EC Number)
	(no 'Enzyme Classificator' available)
		General Enzyme Information	:	BRENDA \| EC-PDB \| Enzyme \| IntEnz
		Pathway	:	KEGG \| MetaCyc

Access by Disease Identifier (MIM ID)
	(no 'MIM ID' available)
		Disease Information	:	OMIM

Access by GenAge ID
	(no 'GenAge ID' available)
		Age Related Information	:	GenAge

Access by PDB/NDB ID
		Domain Information	:	XDom
		Interatomic Contacts of Structural Units	:	CSU
		Ligand-protein Contacts	:	LPC
		Protein Cavities	:	castP
		Sequence and Secondary Structure	:	PDBCartoon
		Structure Alignment	:	STRAP(Java WebStart application, automatic local installation, requires Java; full application with system access!)
		Structure and Sequence Browser	:	STING

Access by UniProt ID/Accession number
	LT_SV40 \| P03070
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

1svl	SAME PROTEIN COMPLEXED WITH ADP
1svo	SAME PROTEIN

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 18)

Sites (18, 18)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (3, 18)

PROSITE Motifs (2, 8)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 6)

CATH Domains (2, 12)

Pfam Domains (1, 6)

Gene Ontology (26, 26)

Visualization

Interactive Views

Still Images

Databases and Analysis Tools

Databases

Analysis Tools

Related Entries

Entries Sharing at Least One Protein Chain (UniProt ID)

Related Entries Specified in the PDB File