1M3Y - JenaLib

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)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   THE STRUCTURE OF MAJOR CAPSID PROTEIN OF A LARGE, LIPID CONTAINING, DNA VIRUS

Authors :   N. Nandhagopal, A. A. Simpson, J. R. Gurnon, X. Yan, T. S. Baker, M. V. Gra J. L. Van Etten, M. G. Rossmann

Date :   01 Jul 02 (Deposition) - 04 Dec 02 (Release) - 13 Jul 11 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.00

Chains :   Asym. Unit : A,B,C,D
Biol. Unit 1: A  (3x)
Biol. Unit 2: B  (3x)
Biol. Unit 3: C  (3x)
Biol. Unit 4: D  (3x)

Keywords :   Major Capsit Protein Vp54, Pbcv-1, Chlorella Virus, Jelly Roll Motif, Glycoprotein, Viral Protein (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   N. Nandhagopal, A. A. Simpson, J. R. Gurnon, X. Yan, T. S. Baker, M. V. Graves, J. L. Van Etten, M. G. Rossmann
The Structure And Evolution Of The Major Capsid Protein Of Large, Lipid-Containing Dna Virus
Proc. Natl. Acad. Sci. Usa V. 99 14758 2002
PubMed-ID: 12411581 | Reference-DOI: 10.1073/PNAS.232580699

Molecule 1 - THE MAJOR CAPSID PROTEIN OF PBCV-1, VP54
	Chains	:	A, B, C, D
	Fragment	:	RESIDUES 25-437
	Organism Scientific	:	PARAMECIUM BURSARIA CHLORELLA VIRUS 1
	Organism Taxid	:	10506
	Other Details	:	HOST VIRUS

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

Summary Information (see also Sequences/Alignments below)

Asymmetric Unit (4, 28)

No.	Name	Count	Type	Full Name
1	HG	8	Ligand/Ion	MERCURY (II) ION
2	MAN	8	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	4	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	NDG	8	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 1 (3, 15)

No.	Name	Count	Type	Full Name
1	HG	-1	Ligand/Ion	MERCURY (II) ION
2	MAN	6	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	NDG	6	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 2 (3, 15)

No.	Name	Count	Type	Full Name
1	HG	-1	Ligand/Ion	MERCURY (II) ION
2	MAN	6	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	NDG	6	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 3 (3, 15)

No.	Name	Count	Type	Full Name
1	HG	-1	Ligand/Ion	MERCURY (II) ION
2	MAN	6	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	NDG	6	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Biological Unit 4 (3, 15)

No.	Name	Count	Type	Full Name
1	HG	-1	Ligand/Ion	MERCURY (II) ION
2	MAN	6	Ligand/Ion	ALPHA-D-MANNOSE
3	NAG	3	Ligand/Ion	N-ACETYL-D-GLUCOSAMINE
4	NDG	6	Ligand/Ion	2-(ACETYLAMINO)-2-DEOXY-A-D-GLUCOPYRANOSE

Asymmetric Unit (28, 28)

No.	Name	Evidence	Residues	Description
01	AC1	SOFTWARE	ASN A:280 , GLY A:289 , THR A:290 , ALA A:293 , THR A:391 , PRO A:393 , MAN A:439	BINDING SITE FOR RESIDUE NDG A 438
02	AC2	SOFTWARE	ALA A:291 , NDG A:438	BINDING SITE FOR RESIDUE MAN A 439
03	AC3	SOFTWARE	SER A:387 , ILE A:388 , ASP A:389 , ALA A:395 , GLY A:398 , ASN A:399 , MAN A:441 , HOH A:453	BINDING SITE FOR RESIDUE NAG A 440
04	AC4	SOFTWARE	NAG A:440	BINDING SITE FOR RESIDUE MAN A 441
05	AC5	SOFTWARE	ASP A:389 , THR A:391 , ASN A:406 , THR A:409	BINDING SITE FOR RESIDUE NDG A 442
06	AC6	SOFTWARE	ASN B:280 , GLY B:289 , THR B:290 , ALA B:293 , THR B:391 , PRO B:393 , MAN B:539	BINDING SITE FOR RESIDUE NDG B 538
07	AC7	SOFTWARE	ALA B:291 , NDG B:538	BINDING SITE FOR RESIDUE MAN B 539
08	AC8	SOFTWARE	SER B:387 , ILE B:388 , ASP B:389 , ALA B:395 , GLY B:398 , ASN B:399 , MAN B:541	BINDING SITE FOR RESIDUE NAG B 540
09	AC9	SOFTWARE	NAG B:540	BINDING SITE FOR RESIDUE MAN B 541
10	BC1	SOFTWARE	ASP B:389 , ASN B:406 , THR B:409	BINDING SITE FOR RESIDUE NDG B 542
11	BC2	SOFTWARE	ASN C:280 , GLY C:289 , THR C:290 , ALA C:293 , THR C:391 , PRO C:393 , MAN C:639 , HOH C:648	BINDING SITE FOR RESIDUE NDG C 638
12	BC3	SOFTWARE	ALA C:291 , NDG C:638	BINDING SITE FOR RESIDUE MAN C 639
13	BC4	SOFTWARE	SER C:387 , ILE C:388 , ASP C:389 , ALA C:395 , GLY C:398 , ASN C:399 , MAN C:641	BINDING SITE FOR RESIDUE NAG C 640
14	BC5	SOFTWARE	NAG C:640	BINDING SITE FOR RESIDUE MAN C 641
15	BC6	SOFTWARE	ASP C:389 , THR C:391 , ASN C:406 , THR C:409	BINDING SITE FOR RESIDUE NDG C 642
16	BC7	SOFTWARE	ASN D:280 , GLY D:289 , THR D:290 , ALA D:293 , THR D:391 , PRO D:393 , MAN D:739 , HOH D:747	BINDING SITE FOR RESIDUE NDG D 738
17	BC8	SOFTWARE	ALA D:291 , NDG D:738	BINDING SITE FOR RESIDUE MAN D 739
18	BC9	SOFTWARE	SER D:387 , ILE D:388 , ASP D:389 , ALA D:395 , GLY D:398 , ASN D:399 , MAN D:741	BINDING SITE FOR RESIDUE NAG D 740
19	CC1	SOFTWARE	NAG D:740	BINDING SITE FOR RESIDUE MAN D 741
20	CC2	SOFTWARE	ASP D:389 , THR D:391 , ASN D:406 , THR D:409	BINDING SITE FOR RESIDUE NDG D 742
21	CC3	SOFTWARE	LEU A:320 , CYS A:369 , ILE A:374	BINDING SITE FOR RESIDUE HG A 443
22	CC4	SOFTWARE	SER A:242 , CYS A:386 , ASN A:406 , THR A:409	BINDING SITE FOR RESIDUE HG A 444
23	CC5	SOFTWARE	LEU B:320 , CYS B:369 , ILE B:374	BINDING SITE FOR RESIDUE HG B 543
24	CC6	SOFTWARE	SER B:242 , CYS B:386 , ASN B:406 , THR B:409	BINDING SITE FOR RESIDUE HG B 544
25	CC7	SOFTWARE	LEU C:320 , CYS C:369 , ILE C:374	BINDING SITE FOR RESIDUE HG C 643
26	CC8	SOFTWARE	SER C:242 , CYS C:386 , ASN C:406 , THR C:409	BINDING SITE FOR RESIDUE HG C 644
27	CC9	SOFTWARE	LEU D:320 , CYS D:369 , ILE D:374	BINDING SITE FOR RESIDUE HG D 743
28	DC1	SOFTWARE	PRO D:241 , SER D:242 , CYS D:386 , ASN D:406 , THR D:409	BINDING SITE FOR RESIDUE HG D 744

(no "SS Bond" information available for 1M3Y)

(no "Cis Peptide Bond" information available for 1M3Y)

(no "SAP(SNP)/Variant" information available for 1M3Y)

(no "PROSITE Motif" information available for 1M3Y)

(no "Exon" information available for 1M3Y)

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:413
 aligned with MCP_PBCV1 | P30328 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:413
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   
            MCP_PBCV1    25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
               SCOP domains d1m3ya1 A:25-221 Major capsid protein vp54                                                                                                                                                           d1m3ya2 A:222-437 Major capsid protein vp54                                                                                                                                                                              SCOP domains
               CATH domains ----------1m3yA01 A:35-222 Adenovirus Type 2 Hexon, domain 4                                                                                                                                          1m3yA02 A:223-437 Major capsid protein Vp54                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeee..........eeeee......eeeeeeeeeeee.........hhhhhheeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee.......hhhhhee.hhh....eeeeeee........ee..ee.......eeeeeeeeeeehhhhhhhhhhh.eeeeeeeee..eee..........eeeeee....eeeeeeeeee...............................hhhhh...hhhhh.eeeeeeee..ee....eehhhhhhhhhhhhh.......eeeee.............ee......eeeeeee.eeee...hhhhhh.....eee.hhhhh.eeeeeeeeeeeeeee.......... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m3y A  25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434

Chain B from PDB  Type:PROTEIN  Length:413
 aligned with MCP_PBCV1 | P30328 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:413
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   
            MCP_PBCV1    25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
               SCOP domains d1m3yb1 B:25-221 Major capsid protein vp54                                                                                                                                                           d1m3yb2 B:222-437 Major capsid protein vp54                                                                                                                                                                              SCOP domains
               CATH domains ----------1m3yB01 B:35-222 Adenovirus Type 2 Hexon, domain 4                                                                                                                                          1m3yB02 B:223-437 Major capsid protein Vp54                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeee..........eeeee......eeeeeeeeeeee.........hhhhhheeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee.......hhhhhee.hhh....eeeeeee........ee..ee.......eeeeeeeeeeehhhhhhhhhhh.eeeeeeeeeeeeee..........eeeeee....eeeeeeeeee...............................hhhhh...hhhhh.eeeeeeee..ee....eehhhhhhhhhhhhh.......eeeee.............ee......eeeeeee.eeee...hhhhhh.....eee.hhhhh.eeeeeeeeeeeeeee..eeee.... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m3y B  25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434

Chain C from PDB  Type:PROTEIN  Length:413
 aligned with MCP_PBCV1 | P30328 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:413
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   
            MCP_PBCV1    25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
               SCOP domains d1m3yc1 C:25-221 Major capsid protein vp54                                                                                                                                                           d1m3yc2 C:222-437 Major capsid protein vp54                                                                                                                                                                              SCOP domains
               CATH domains ----------1m3yC01 C:35-222 Adenovirus Type 2 Hexon, domain 4                                                                                                                                          1m3yC02 C:223-437 Major capsid protein Vp54                                                                                                                                                                             CATH domains
               Pfam domains ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ............eeeeeeee..........eeeee......eeeeeeeeeeee.........hhhhhheeeeeeee..eeeeeeehhhhhhhhhhhhhhhhhhhhhhhhh.........eeeeeee.......hhhhhee.hhh....eeeeeee.....................eeeeeeeeeeehhhhhhhhhhh............................................................................hhhhh...hhhhh...................hhhhhhhhhhhhh................................................hhhhhh.........hhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m3y C  25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434

Chain D from PDB  Type:PROTEIN  Length:413
 aligned with MCP_PBCV1 | P30328 from UniProtKB/Swiss-Prot  Length:437

    Alignment length:413
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434   
            MCP_PBCV1    25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
               SCOP domains d1m3yd1 D:25-221 Major capsid protein vp54                                                                                                                                                           d1m3yd2 D:222-437 Major capsid protein vp54                                                                                                                                                                              SCOP domains
               CATH domains ----------1m3yD01 D:35-222 Adenovirus Type 2 Hexon, domain 4                                                                                                                                          1m3yD02 D:223-437 Major capsid protein Vp54                                                                                                                                                                             CATH domains
           Pfam domains (1) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------Capsid_NCLDV-1m3yD01 D:196-433                                                                                                                                                                                                                ---- Pfam domains (1)
           Pfam domains (2) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------Capsid_NCLDV-1m3yD02 D:196-433                                                                                                                                                                                                                ---- Pfam domains (2)
           Pfam domains (3) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------Capsid_NCLDV-1m3yD03 D:196-433                                                                                                                                                                                                                ---- Pfam domains (3)
           Pfam domains (4) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------Capsid_NCLDV-1m3yD04 D:196-433                                                                                                                                                                                                                ---- Pfam domains (4)
         Sec.struct. author ..............................................................hhhhhh.................hhhhhhhhhhhhhhhhhhhhhhhhh.......................hhhhh...hhh...........................................hhhhhhhhhhh............................................................................hhhhh...hhhhh...................hhhhhhhhhhhhh................................................hhhhhh.........hhhhh.......................... Sec.struct. author
                 SAPs(SNPs) ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 1m3y D  25 TFFKTVYRRYTNFAIESIQQTINGSVGFGNKVSTQISRNGDLITDIVVEFVLTKGGNGGTTYYPAEELLQDVELEIGGQRIDKHYNDWFRTYDALFRMNDDRYNYRRMTDWVNNELVGAQKRFYVPLIFFFNQTPGLALPLIALQYHEVKLYFTLASQVQGVNYNGSSAIAGAAQPTMSVWVDYIFLDTQERTRFAQLPHEYLIEQLQFTGSETATPSATTQASQNIRLNFNHPTKYLAWNFNNPTNYGQYTALANIPGACSGAGTAAATVTTPDYGNTGTYNEQLAVLDSAKIQLNGQDRFATRKGSYFNKVQPYQSIGGVTPAGVYLYSFALKPAGRQPSGTCNFSRIDNATLSLTYKTCSIDATSPAAVLGNTETVTANTATLLTALNIYAKNYNVLRIMSGMGGLAYAN 437
                                    34        44        54        64        74        84        94       104       114       124       134       144       154       164       174       184       194       204       214       224       234       244       254       264       274       284       294       304       314       324       334       344       354       364       374       384       394       404       414       424       434

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 II dsDNA viruses VP (10)

Family: Major capsid protein vp54 (2)

Protein domain: Major capsid protein vp54 (2)

Paramecium bursaria chlorella virus 1, PBCV-1 [TaxId: 10506] (2)

1a	d1m3ya1	A:25-221
1b	d1m3ya2	A:222-437
1c	d1m3yb1	B:25-221
1d	d1m3yb2	B:222-437
1e	d1m3yc1	C:25-221
1f	d1m3yc2	C:222-437
1g	d1m3yd1	D:25-221
1h	d1m3yd2	D:222-437

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Mainly Beta (13760)

Architecture: Distorted Sandwich (506)

Topology: Adenovirus Type 2 Hexon; domain 4 (7)

Homologous Superfamily: Adenovirus Type 2 Hexon, domain 4 (4)

Paramecium bursaria chlorella virus 1. Organism_taxid: 10506. (1)

1a	1m3yA01	A:35-222
1b	1m3yB01	B:35-222
1c	1m3yC01	C:35-222
1d	1m3yD01	D:35-222

Homologous Superfamily: Major capsid protein Vp54 (2)

Paramecium bursaria chlorella virus 1. Organism_taxid: 10506. (1)

2a	1m3yA02	A:223-437
2b	1m3yB02	B:223-437
2c	1m3yC02	C:223-437
2d	1m3yD02	D:223-437

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: no clan defined [family: Capsid_NCLDV] (2)

Family: Capsid_NCLDV (2)

Paramecium bursaria Chlorella virus 1 (PBCV-1) (2)

1a	Capsid_NCLDV-1m3yD01	D:196-433
1b	Capsid_NCLDV-1m3yD02	D:196-433
1c	Capsid_NCLDV-1m3yD03	D:196-433
1d	Capsid_NCLDV-1m3yD04	D:196-433

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (MCP_PBCV1 | P30328)

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.
cellular component
	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
		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
		HG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		MAN	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NAG	[ RasMol \| Jena3D ]	+environment [ RasMol \| Jena3D ]
		NDG	[ 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 ]
		CC1	[ RasMol ]	+environment [ RasMol ]
		CC2	[ RasMol ]	+environment [ RasMol ]
		CC3	[ RasMol ]	+environment [ RasMol ]
		CC4	[ RasMol ]	+environment [ RasMol ]
		CC5	[ RasMol ]	+environment [ RasMol ]
		CC6	[ RasMol ]	+environment [ RasMol ]
		CC7	[ RasMol ]	+environment [ RasMol ]
		CC8	[ RasMol ]	+environment [ RasMol ]
		CC9	[ RasMol ]	+environment [ RasMol ]
		DC1	[ RasMol ]	+environment [ RasMol ]

	Cis Peptide Bonds
(no "Cis Peptide Bonds" information available for 1m3y)

Biological Units
	Complete Structure
		Biological Unit 1	[ Jena3D ]
		Biological Unit 2	[ Jena3D ]
		Biological Unit 3	[ Jena3D ]
		Biological Unit 4	[ Jena3D ]

Jmol
	protein: cartoon or spacefill or dots and stick; nucleic acid: cartoon and stick; ligands: spacefill; active site: stick [ Asym. Unit PNG format \| Asym. Unit - sites PNG format \| Biol. Unit 1 PNG format \| Biol. Unit 1 - sites PNG format \| Biol. Unit 2 PNG format \| Biol. Unit 3 PNG format \| Biol. Unit 4 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
	1m3y
		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
	MCP_PBCV1 \| P30328
		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
	MCP_PBCV1 \| P30328
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	MCP_PBCV1 \| P30328	:	1j5q 1m4x 3kk5

1j5q	THE SAME PROTEIN SOLVED IN DIFFERENT SPACE GROUP
1m4x	THE SAME PROTEIN STUDIED BY CRYO-ELECTRON MICROSCOPY

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (4, 28)

Sites (28, 28)

SS Bonds (0, 0)

Cis Peptide Bonds (0, 0)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (0, 0)

PROSITE Motifs (0, 0)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (1, 8)

CATH Domains (2, 8)

Pfam Domains (1, 4)

Gene Ontology (3, 3)

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