1VPS - JenaLib

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Asymmetric Unit (Jmol Viewer)

Asym. Unit - sites (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biol. Unit 1 - sites (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Title :   POLYOMAVIRUS VP1 PENTAMER COMPLEXED WITH A DISIALYLATED HEXASACCHARIDE

Authors :   T. Stehle, S. C. Harrison

Date :   07 Mar 97 (Deposition) - 15 May 97 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   1.90

Chains :   Asym. Unit : A,B,C,D,E
Biol. Unit 1: A,B,C,D,E  (1x)
Biol. Unit 2: A,B,C,D,E  (2x)

Keywords :   Virus Coat Protein, Oligosaccharide Binding, Virus Assembly, Sialic Acid, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   T. Stehle, S. C. Harrison
High-Resolution Structure Of A Polyomavirus Vp1-Oligosaccharide Complex: Implications For Assembly And Receptor Binding.
Embo J. V. 16 5139 1997
PubMed-ID: 9305654 | Reference-DOI: 10.1093/EMBOJ/16.16.5139
(for further references see the PDB file header)

Molecule 1 - POLYOMAVIRUS VP1 PENTAMER
	Chains	:	A, B, C, D, E
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Organism Scientific	:	MURINE POLYOMAVIRUS
	Organism Taxid	:	10634

		1	2	3	4	5
Asymmetric Unit	:	A	B	C	D	E
Biological Unit 1 (1x)	:	A	B	C	D	E
Biological Unit 2 (2x)	:	A	B	C	D	E

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (3, 20)

No.	Name	Count	Type	Full Name
1	GAL	5	Ligand/Ion	BETA-D-GALACTOSE
2	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SIA	10	Ligand/Ion	O-SIALIC ACID

Biological Unit 1 (3, 20)

No.	Name	Count	Type	Full Name
1	GAL	5	Ligand/Ion	BETA-D-GALACTOSE
2	NAG	5	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SIA	10	Ligand/Ion	O-SIALIC ACID

Biological Unit 2 (3, 40)

No.	Name	Count	Type	Full Name
1	GAL	10	Ligand/Ion	BETA-D-GALACTOSE
2	NAG	10	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
3	SIA	20	Ligand/Ion	O-SIALIC ACID

Asymmetric Unit (20, 20)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	GAL A:2 , TYR A:72 , ARG A:77 , GLY A:78 , THR A:291 , ASN A:293 , HIS A:298 , HOH A:496 , HOH A:499 , HOH A:603 , HOH A:662 , HOH A:669 , HOH A:678 , ASP B:85	BINDING SITE FOR RESIDUE SIA A 1
02	AC2	SOFTWARE	SIA A:1 , NAG A:3 , GLY A:78 , ASN A:93 , THR A:94 , HOH A:660 , HOH A:662 , HOH A:663	BINDING SITE FOR RESIDUE GAL A 2
03	AC3	SOFTWARE	GAL A:2 , SIA A:4	BINDING SITE FOR RESIDUE NAG A 3
04	AC4	SOFTWARE	NAG A:3 , ASN A:80 , LEU A:81 , THR A:83 , SER A:89 , LYS A:186 , HOH A:400 , HOH A:414 , HOH A:698	BINDING SITE FOR RESIDUE SIA A 4
05	AC5	SOFTWARE	GAL B:2 , TYR B:72 , ARG B:77 , GLY B:78 , THR B:291 , ASN B:293 , HIS B:298 , HOH B:518 , HOH B:521 , HOH B:570 , HOH B:714 , HOH B:715 , HOH B:725 , ASP C:85	BINDING SITE FOR RESIDUE SIA B 1
06	AC6	SOFTWARE	SIA B:1 , NAG B:3 , GLY B:78 , ASN B:93 , THR B:94 , HOH B:659 , HOH B:684 , HOH B:713 , HOH B:714	BINDING SITE FOR RESIDUE GAL B 2
07	AC7	SOFTWARE	GAL B:2 , SIA B:4 , HOH B:713	BINDING SITE FOR RESIDUE NAG B 3
08	AC8	SOFTWARE	NAG B:3 , ASN B:80 , LEU B:81 , THR B:83 , SER B:89 , LYS B:186 , HOH B:434 , HOH B:711 , HOH B:712	BINDING SITE FOR RESIDUE SIA B 4
09	AC9	SOFTWARE	GAL C:2 , TYR C:72 , ARG C:77 , GLY C:78 , THR C:291 , ASN C:293 , HIS C:298 , HOH C:512 , HOH C:515 , HOH C:579 , HOH C:724 , HOH C:747 , HOH C:758 , ASP D:85	BINDING SITE FOR RESIDUE SIA C 1
10	BC1	SOFTWARE	SIA C:1 , NAG C:3 , GLY C:78 , ASN C:93 , THR C:94 , HOH C:598 , HOH C:626 , HOH C:724 , HOH C:726	BINDING SITE FOR RESIDUE GAL C 2
11	BC2	SOFTWARE	GAL C:2 , SIA C:4 , HOH C:598	BINDING SITE FOR RESIDUE NAG C 3
12	BC3	SOFTWARE	NAG C:3 , ASN C:80 , LEU C:81 , SER C:89 , HOH C:418 , HOH C:432 , HOH C:749	BINDING SITE FOR RESIDUE SIA C 4
13	BC4	SOFTWARE	GAL D:2 , TYR D:72 , ARG D:77 , GLY D:78 , THR D:291 , ASN D:293 , HIS D:298 , HOH D:523 , HOH D:526 , HOH D:634 , HOH D:719 , HOH D:720 , HOH D:735 , HOH D:742 , HOH D:749 , ASP E:85	BINDING SITE FOR RESIDUE SIA D 1
14	BC5	SOFTWARE	SIA D:1 , NAG D:3 , GLY D:78 , ASN D:93 , THR D:94 , HOH D:717 , HOH D:720 , HOH D:726	BINDING SITE FOR RESIDUE GAL D 2
15	BC6	SOFTWARE	TYR C:294 , GAL D:2 , SIA D:4 , HOH D:734 , HOH D:740	BINDING SITE FOR RESIDUE NAG D 3
16	BC7	SOFTWARE	ASN B:149 , HOH B:650 , TYR C:294 , NAG D:3 , ASN D:80 , LEU D:81 , THR D:83 , SER D:89 , LYS D:186 , HOH D:628 , HOH D:718 , HOH D:728	BINDING SITE FOR RESIDUE SIA D 4
17	BC8	SOFTWARE	ASP A:85 , GAL E:2 , TYR E:72 , ARG E:77 , GLY E:78 , THR E:291 , ASN E:293 , HIS E:298 , HOH E:528 , HOH E:531 , HOH E:595 , HOH E:668 , HOH E:672	BINDING SITE FOR RESIDUE SIA E 1
18	BC9	SOFTWARE	SIA E:1 , NAG E:3 , GLY E:78 , ASN E:93 , THR E:94 , HOH E:668 , HOH E:670	BINDING SITE FOR RESIDUE GAL E 2
19	CC1	SOFTWARE	GAL E:2 , SIA E:4 , HOH E:698	BINDING SITE FOR RESIDUE NAG E 3
20	CC2	SOFTWARE	NAG E:3 , ASN E:80 , LEU E:81 , THR E:83 , SER E:89 , HOH E:435 , HOH E:665	BINDING SITE FOR RESIDUE SIA E 4

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

Asymmetric Unit

No.	Residues
1	Thr A:62	-	Pro A:63
2	Thr B:62	-	Pro B:63
3	Thr C:62	-	Pro C:63
4	Thr D:62	-	Pro D:63
5	Thr E:62	-	Pro E:63

(no "SAP(SNP)/Variant" information available for 1VPS)

(no "PROSITE Motif" information available for 1VPS)

(no "Exon" information available for 1VPS)

Asymmetric 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:285
 aligned with VP1_POVMP | P49302 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:285
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312     
            VP1_POVMP    33 GGMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK 317
               SCOP domains d1vpsa_ A: Polyomavirus coat proteins                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1vpsA00 A:32-316 Polyomavirus Vp1, chain A                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeee................hhh...................hhh....eeeeee............eeeeeeeeeeeeee.hhhhh........................eeeeeeee...eeeee................hhhhh.....hhhh......eeee..........eee.......eeeeeeee.......eeeee....................eeeeeeeeeeeeee......eeeee.eeeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vps A  32 GGMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK 316
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

Chain B from PDB  Type:PROTEIN  Length:289
 aligned with VP1_POVMP | P49302 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:289
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312         
            VP1_POVMP    33 GGMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVKNPYP 321
               SCOP domains d1vpsb_ B: Polyomavirus coat proteins                                                                                                                                                                                                                                                             SCOP domains
               CATH domains 1vpsB00 B:32-320 Polyomavirus Vp1, chain A                                                                                                                                                                                                                                                        CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeee................hhh...................hhh....eeeeee...........eeeeeeeeeeeeee..hhhhh........................eeeeeeee...eeeee................hhhhh.....hhhh......eeee..........eee.......eeeeeeee.......eeeee....................eeeeeeeeeeeeee......eeeee..eeeeeeeeeeeee.... Sec.struct. author
                 SAPs(SNPs) ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vps B  32 GGMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVKNPYP 320
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

Chain C from PDB  Type:PROTEIN  Length:285
 aligned with VP1_POVMP | P49302 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:285
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312     
            VP1_POVMP    33 GGMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK 317
               SCOP domains d1vpsc_ C: Polyomavirus coat proteins                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1vpsC00 C:32-316 Polyomavirus Vp1, chain A                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeee................hhh...................hhh....eeeeee............eeeeeeeeeeeee..hhhhh........................eeeeeeee...eeeee................hhhhh.....hhhh......eeee..........eee.......eeeeeeee.......eeeee....................eeeeeeeeeeeeee......eeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vps C  32 GGMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK 316
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

Chain D from PDB  Type:PROTEIN  Length:285
 aligned with VP1_POVMP | P49302 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:285
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312     
            VP1_POVMP    33 GGMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK 317
               SCOP domains d1vpsd_ D: Polyomavirus coat proteins                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1vpsD00 D:32-316 Polyomavirus Vp1, chain A                                                                                                                                                                                                                                                    CATH domains
               Pfam domains --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ..............eeeeeeee................hhh...................hhh....eeeeee............eeeeeeeeeeeee..hhhhh........................eeeeeeee...eeeee................hhhhh.....hhhh......eeee..........eee.......eeeeeeee.......eeeee....................eeeeeeeeeeeeee......eeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vps D  32 GGMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK 316
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

Chain E from PDB  Type:PROTEIN  Length:285
 aligned with VP1_POVMP | P49302 from UniProtKB/Swiss-Prot  Length:384

    Alignment length:285
                                    42        52        62        72        82        92       102       112       122       132       142       152       162       172       182       192       202       212       222       232       242       252       262       272       282       292       302       312     
            VP1_POVMP    33 GGMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK 317
               SCOP domains d1vpse_ E: Polyomavirus coat proteins                                                                                                                                                                                                                                                         SCOP domains
               CATH domains 1vpsE00 E:32-316 Polyomavirus Vp1, chain A                                                                                                                                                                                                                                                    CATH domains
           Pfam domains (1) Polyoma_coat-1vpsE01 E:32-316                                                                                                                                                                                                                                                                 Pfam domains (1)
           Pfam domains (2) Polyoma_coat-1vpsE02 E:32-316                                                                                                                                                                                                                                                                 Pfam domains (2)
           Pfam domains (3) Polyoma_coat-1vpsE03 E:32-316                                                                                                                                                                                                                                                                 Pfam domains (3)
           Pfam domains (4) Polyoma_coat-1vpsE04 E:32-316                                                                                                                                                                                                                                                                 Pfam domains (4)
           Pfam domains (5) Polyoma_coat-1vpsE05 E:32-316                                                                                                                                                                                                                                                                 Pfam domains (5)
         Sec.struct. author ..............eeeeeeee................hhh...................hhh....eeeeee............eeeeeeeeeeeee..hhhhh........................eeeeeeee....eeee................hhhhh.....hhhh......eee...........eee.......eeeeeeee.......eeeee....................eeeeeeeeeeeeee......eeeee..eeeeeeeeeeee. Sec.struct. author
                 SAPs(SNPs) --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript --------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1vps E  32 GGMEVLDLVTGPDSVTEIEAFLNPRMGQPPTPESLTEGGQYYGWSRGINLATSDTEDSPGNNTLPTWSMAKLQLPMLNEDLTCDTLQMWEAVSVKTEVVGSGSLLDVHGFNKPTDTVNTKGISTPVEGSQYHVFAVGGEPLDLQGLVTDARTKYKEEGVVTIKTITKKDMVNKDQVLNPISKAKLDKDGMYPVEIWHPDPAKNENTRYFGNYTGGTTTPPVLQFTNTLTTVLLDENGVGPLCKGEGLYLSCVDIMGWRVTRNYDVHHWRGLPRYFKITLRKRWVK 316
                                    41        51        61        71        81        91       101       111       121       131       141       151       161       171       181       191       201       211       221       231       241       251       261       271       281       291       301       311

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 Unit

Classes(

)

Folds(

)

Superfamilies( (-)

)

Families(

)

Protein Domains( (-)

)

Organisms( (-)

)

Class: All beta proteins (24004)

Fold: Nucleoplasmin-like/VP (viral coat and capsid proteins) (278)

Superfamily: Group I dsDNA viruses (30)

Family: Papovaviridae-like VP (19)

Protein domain: Polyomavirus coat proteins (6)

Murine polyomavirus, strain small-plaque 16 [TaxId: 10634] (5)

1a	d1vpsa_	A:
1b	d1vpsb_	B:
1c	d1vpsc_	C:
1d	d1vpsd_	D:
1e	d1vpse_	E:

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Sandwich (5577)

Topology: Polyomavirus Vp1; Chain A (9)

Homologous Superfamily: Polyomavirus Vp1, chain A (8)

Murine polyomavirus. Organism_taxid: 10634. (2)

1a	1vpsB00	B:32-320
1b	1vpsA00	A:32-316
1c	1vpsC00	C:32-316
1d	1vpsD00	D:32-316
1e	1vpsE00	E:32-316

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Polyoma_coat] (8)

Family: Polyoma_coat (8)

Murine polyomavirus (strain P16 small-plaque) (MPyV) (4)

1a	Polyoma_coat-1vpsE01	E:32-316
1b	Polyoma_coat-1vpsE02	E:32-316
1c	Polyoma_coat-1vpsE03	E:32-316
1d	Polyoma_coat-1vpsE04	E:32-316
1e	Polyoma_coat-1vpsE05	E:32-316

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D,E (VP1_POVMP | P49302)

molecular function
	GO:0005198	structural molecule activity	The action of a molecule that contributes to the structural integrity of a complex or its assembly within or outside a cell.
biological process
	GO:0075513	caveolin-mediated endocytosis of virus by host cell	Any caveolin-mediated endocytosis that is involved in the uptake of a virus into a host cell. Begins when material is taken up into plasma membrane caveolae - specialized lipid rafts that form 50-70 nm flask-shaped invaginations of the plasma membrane - which then pinch off to form endocytic caveolar carriers containing the virus.
	GO:0075509	endocytosis involved in viral entry into host cell	Any endocytosis that is involved in the uptake of a virus into a host cell.
	GO:0046718	viral entry into host cell	The process that occurs after viral attachment by which a virus, or viral nucleic acid, breaches the plasma membrane or cell envelope and enters the host cell. The process ends when the viral nucleic acid is released into the host cell cytoplasm.
	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.
	GO:0019062	virion attachment to host cell	The process by which a virion protein binds to molecules on the host cellular surface or host cell surface projection.
cellular component
	GO:0039620	T=7 icosahedral viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles where the subunits (capsomeres) are arranged to form an icosahedron with T=7 symmetry. The T=7 capsid is composed of 12 pentameric and 60 hexameric capsomeres.
	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.
	GO:0019028	viral capsid	The protein coat that surrounds the infective nucleic acid in some virus particles. It comprises numerous regularly arranged subunits, or capsomeres.
	GO:0019012	virion	The complete fully infectious extracellular virus particle.

Asymmetric Unit
	Complete Structure
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	Ligands, Modified Residues, Ions
		GAL	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
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	Cis Peptide Bonds
		Thr A:62 - Pro A:63	[ RasMol ]
		Thr B:62 - Pro B:63	[ RasMol ]
		Thr C:62 - Pro C:63	[ RasMol ]
		Thr D:62 - Pro D:63	[ RasMol ]
		Thr E:62 - Pro E:63	[ RasMol ]

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	VP1_POVMP \| P49302
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	VP1_POVMP \| P49302	:	1cn3 1sid 1sie 1vpn 5cpu 5cpw 5cpx 5cpy 5cpz 5cq0

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Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (3, 20)

Sites (20, 20)

SS Bonds (0, 0)

Cis Peptide Bonds (5, 5)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

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Exons (0, 0)

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