2PZS - JenaLib

Biol.Unit 1 - manually (Jmol Viewer)

Asymmetric Unit (Jmol Viewer)

Biological Unit 1 (Jmol Viewer)

Biological Unit 2 (Jmol Viewer)

Biological Unit 3 (Jmol Viewer)

Biological Unit 4 (Jmol Viewer)

Title :   PHI29 DNA POLYMERASE COMPLEXED WITH PRIMER-TEMPLATE DNA (POST-TRANSLOCATION BINARY COMPLEX)

Authors :   A. J. Berman, S. Kamtekar, J. L. Goodman, J. M. Lazaro, M. De Vega, L. Blanco, M. Salas, T. A. Steitz

Date :   18 May 07 (Deposition) - 17 Jul 07 (Release) - 24 Feb 09 (Revision)

Method :   X-RAY DIFFRACTION

Resolution :   2.60

Chains :   Asym. Unit : A,B,C,D,R,S,T,U,X,Y
Biol. Unit 1: A,X,Y  (1x)
Biol. Unit 2: B,T  (1x)
Biol. Unit 3: C,U  (1x)
Biol. Unit 4: D,R,S  (1x)

Keywords :   Protein-Dna Complex, Replication, Transferase/Dna Complex (Keyword Search: [Gene Ontology, PubMed, Web (Google)] )

Reference :   A. J. Berman, S. Kamtekar, J. L. Goodman, J. M. Lazaro, M. De Vega, L. Blanco, M. Salas, T. A. Steitz
Structures Of Phi29 Dna Polymerase Complexed With Substrate: The Mechanism Of Translocation In B-Family Polymerases
Embo J. V. 26 3494 2007
PubMed-ID: 17611604 | Reference-DOI: 10.1038/SJ.EMBOJ.7601780
(for further references see the PDB file header)

Molecule 1 - 5'-D(GACTGCTTAC)-3'
	Chains	:	X, R
	Engineered	:	YES
	Synthetic	:	YES

Molecule 2 - 5'-D(CTAACACGTAAGCAGTC)-3'
	Chains	:	Y, T, U, S
	Engineered	:	YES
	Synthetic	:	YES

Molecule 3 - DNA POLYMERASE
	Chains	:	A, B, C, D
	EC Number	:	2.7.7.7
	Engineered	:	YES
	Expression System	:	ESCHERICHIA COLI
	Expression System Taxid	:	562
	Gene	:	2, GP2
	Mutation	:	YES
	Organism Scientific	:	BACILLUS PHAGE PHI29
	Organism Taxid	:	10756
	Synonym	:	EARLY PROTEIN GP2

		1	2	3	4	5	6	7	8	9	10
Asymmetric Unit	:	A	B	C	D	R	S	T	U	X	Y
Biological Unit 1 (1x)	:	A								X	Y
Biological Unit 2 (1x)	:		B					T
Biological Unit 3 (1x)	:			C					U
Biological Unit 4 (1x)	:				D	R	S

Summary Information (see also Sequences/Alignments below)

(no "Ligand,Modified Residues,Ions" information available for 2PZS)

(no "Site" information available for 2PZS)

(no "SS Bond" information available for 2PZS)

Asymmetric Unit

No.	Residues
1	Phe C:292	-	Glu C:293

Asymmetric Unit (2, 8)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DPOL_BPPH2_001 *	A	176	R	DPOL_BPPH2	---	---	A/B/C/D	A	176	R
2	UniProt	VAR_DPOL_BPPH2_002 *	A	355	V	DPOL_BPPH2	---	---	A/B/C/D	A	355	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 1 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DPOL_BPPH2_001 *	A	176	R	DPOL_BPPH2	---	---	A	A	176	R
2	UniProt	VAR_DPOL_BPPH2_002 *	A	355	V	DPOL_BPPH2	---	---	A	A	355	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 2 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DPOL_BPPH2_001 *	A	176	R	DPOL_BPPH2	---	---	B	A	176	R
2	UniProt	VAR_DPOL_BPPH2_002 *	A	355	V	DPOL_BPPH2	---	---	B	A	355	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 3 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DPOL_BPPH2_001 *	A	176	R	DPOL_BPPH2	---	---	C	A	176	R
2	UniProt	VAR_DPOL_BPPH2_002 *	A	355	V	DPOL_BPPH2	---	---	C	A	355	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Biological Unit 4 (2, 2)

								dbSNP	PDB
No.	Source	Variant ID	Variant			UniProt ID	Status	ID	Chain	Variant
1	UniProt	VAR_DPOL_BPPH2_001 *	A	176	R	DPOL_BPPH2	---	---	D	A	176	R
2	UniProt	VAR_DPOL_BPPH2_002 *	A	355	V	DPOL_BPPH2	---	---	D	A	355	V
	* ID not provided by source

SNP/SAP Summary Statistics (UniProtKB/Swiss-Prot)

Asymmetric Unit (1, 4)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_B	PS00116	DNA polymerase family B signature.	DPOL_BPPH2	454-462	4	A:454-462 B:454-462 C:454-462 D:454-462

Biological Unit 1 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_B	PS00116	DNA polymerase family B signature.	DPOL_BPPH2	454-462	1	A:454-462 - - -

Biological Unit 2 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_B	PS00116	DNA polymerase family B signature.	DPOL_BPPH2	454-462	1	- B:454-462 - -

Biological Unit 3 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_B	PS00116	DNA polymerase family B signature.	DPOL_BPPH2	454-462	1	- - C:454-462 -

Biological Unit 4 (1, 1)

	PROSITE			UniProtKB		PDB
No.	ID	AC	Description	ID	Location	Count	Location
1	DNA_POLYMERASE_B	PS00116	DNA polymerase family B signature.	DPOL_BPPH2	454-462	1	- - - D:454-462

(no "Exon" information available for 2PZS)

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:571
 aligned with DPOL_BPPH2 | P03680 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:571
                                    14        24        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       444       454       464       474       484       494       504       514       524       534       544       554       564       574 
           DPOL_BPPH2     5 PRKMYSCDFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK 575
               SCOP domains d2pzsa1 A:5-187 Exonuclease domain of phi29 DNA polymerase                                                                                                                             d2pzsa2 A:188-575 phi29 DNA polymerase                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2pzsA01 A:5-188  [code=3.30.420.10, no name defined]                                                                                                                                    2pzsA02 A:189-261,A:426-531 Palm domain of DNA polymerase                2pzsA03 A:262-359 TPR 1 domain of DNA polymerase                                                  2pzsA04 A:360-395 Helix hairpin bin 2pzsA05 A:396-425             2pzsA02 A:189-261,A:426-531 Palm domain of DNA polymerase                                                 2pzsA06 A:532-575 DNA polymerase; domain 6   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee........eeeeeeee..eeeeeeee.hhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..ee.......eeeeee.....eeeeeeeeeee..eeeeeeeeehhhhh..hhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhhh....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh......eee.hhhh......eeeeee.hhhhhhhhhh.eeeeeeeeee..........eeeeeeeeeeee.............................eeeeeehhhhhhhhhheeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh........eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee.......hhhhh.......eeeeeeeeeeeeee..eeeeeeeeee....eee.......eeeeeeee...hhhhhh...........eeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzs A   5 PRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK 575
                                    14        24        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       444       454       464       474       484       494       504       514       524       534       544       554       564       574

Chain B from PDB  Type:PROTEIN  Length:566
 aligned with DPOL_BPPH2 | P03680 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:571
                                    14        24        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       444       454       464       474       484       494       504       514       524       534       544       554       564       574 
           DPOL_BPPH2     5 PRKMYSCDFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK 575
               SCOP domains d2pzsb1 B:5-187 Exonuclease domain of phi29 DNA polymerase                                                                                                                             d2pzsb2 B:188-575 phi29 DNA polymerase                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2pzsB01 B:5-188  [code=3.30.420.10, no name defined]                                                                                                                                    2pzsB02 B:189-261,B:426-531 Palm domain of DNA polymerase                2pzsB03 B:262-359 TPR 1 domain of DNA polyme     rase                                             2pzsB04 B:360-395 Helix hairpin bin 2pzsB05 B:396-425             2pzsB02 B:189-261,B:426-531 Palm domain of DNA polymerase                                                 2pzsB06 B:532-575 DNA polymerase; domain 6   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee........eeeeeeee......eeee.hhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..ee.......eeeeee.....eeeeeeeeeee..eeeeeeeee.hhh...hhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh......eee.hhhh.eee..eeeeee.hhhhhhhhhh.eeeeeeeeee..........eeeeeeeeeeee...........-----.............eeeeeehhhhhhhhhheeeeeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee....hhhhhh.........eeeeeeeeeeeeee..eeeeeeeeeee..eeee.......eeeeeeee...hhhhhhhhhhhhh....eeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzs B   5 PRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIK-----KGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK 575
                                    14        24        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       444       454       464       474       484       494       504       514       524       534       544       554       564       574 
                                                                                                                                                                                                                                                                                                                                      305   311

Chain C from PDB  Type:PROTEIN  Length:563
 aligned with DPOL_BPPH2 | P03680 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:571
                                    14        24        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       444       454       464       474       484       494       504       514       524       534       544       554       564       574 
           DPOL_BPPH2     5 PRKMYSCDFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK 575
               SCOP domains d2pzsc1 C:5-187 Exonuclease domain of phi29 DNA polymerase                                                                                                                             d2pzsc2 C:188-575 phi29 DNA polymerase                                                                                                                                                                                                                                                                                                                                                               SCOP domains
               CATH domains 2pzsC01 C:5-188  [code=3.30.420.10, no name defined]                                                                                                                                    2pzsC02 C:189-261,C:426-531 Palm domain of DNA polymerase                2pzsC03 C:262-359 TPR 1 domain of DNA polyme        rase                                          2pzsC04 C:360-395 Helix hairpin bin 2pzsC05 C:396-425             2pzsC02 C:189-261,C:426-531 Palm domain of DNA polymerase                                                 2pzsC06 C:532-575 DNA polymerase; domain 6   CATH domains
               Pfam domains ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Pfam domains
         Sec.struct. author ...eeeeeeee........eeeeeeee......eeee.hhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhh....ee.......eeeeee.....eeeeeeeeeee..eeeeeeeeehhhhh..hhhhhhhhhh....................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh......eee.hhhh.eee..eeeeee.hhhhhhhhhh.eeeeeeeeee..........eeeeeeeee..............--------..........eeeeeehhhhhhhhhhh..eeeeeeeeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh......eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee....hhhhhhhh.......eeeeeeeeeeeeee..eeeeeeeeeee..eeee.......eeeeeeee...hhhhhh...........eeeeeeeeeee..eeeeeeeeee.. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V---------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM----------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- Transcript
                 2pzs C   5 PRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIK--------EYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK 575
                                    14        24        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       444       454       464       474       484       494       504       514       524       534       544       554       564       574 
                                                                                                                                                                                                                                                                                                                                      305      314

Chain D from PDB  Type:PROTEIN  Length:564
 aligned with DPOL_BPPH2 | P03680 from UniProtKB/Swiss-Prot  Length:575

    Alignment length:570
                                    14        24        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       444       454       464       474       484       494       504       514       524       534       544       554       564       574
           DPOL_BPPH2     5 PRKMYSCDFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFDGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTI 574
               SCOP domains d2pzsd1 D:5-187 Exonuclease domain of phi29 DNA polymerase                                                                                                                             d2pzsd2 D:188-574 phi29 DNA polymerase                                                                                                                                                                                                                                                                                                                                                              SCOP domains
               CATH domains 2pzsD01 D:5-188  [code=3.30.420.10, no name defined]                                                                                                                                    2pzsD02 D:189-261,D:426-531 Palm domain of DNA polymerase                2pzsD03 D:262-359 TPR 1 domain of DNA polyme    r  ase                                            2pzsD04 D:360-395 Helix hairpin bin 2pzsD05 D:396-425             2pzsD02 D:189-261,D:426-531 Palm domain of DNA polymerase                                                 2pzsD06 D:532-574 DNA polymerase; domain 6  CATH domains
           Pfam domains (1) --------------------------------------------DNA_pol_B_2-2pzsD01 D:49-488                                                                                                                                                                                                                                                                                                                                                                                                                            -------------------------------------------------------------------------------------- Pfam domains (1)
           Pfam domains (2) --------------------------------------------DNA_pol_B_2-2pzsD02 D:49-488                                                                                                                                                                                                                                                                                                                                                                                                                            -------------------------------------------------------------------------------------- Pfam domains (2)
           Pfam domains (3) --------------------------------------------DNA_pol_B_2-2pzsD03 D:49-488                                                                                                                                                                                                                                                                                                                                                                                                                            -------------------------------------------------------------------------------------- Pfam domains (3)
           Pfam domains (4) --------------------------------------------DNA_pol_B_2-2pzsD04 D:49-488                                                                                                                                                                                                                                                                                                                                                                                                                            -------------------------------------------------------------------------------------- Pfam domains (4)
         Sec.struct. author ...eeeeeeee........eeeeeeee..eeeeeeee.hhhhhhhhhhhhh.eeee.hhhhhhhhhhhhhhhh..ee.......eeeeee.....eeeeeeeeeee..eeeeeeeee.......hhhhhhhhh.....................hhhhhhhhhhhhhhhhhhhhhhhhh.....hhhhhhhhhhhhhhhhhhhhhhh...hhhhhhhhhh......eee.hhhh......eeeeee.hhhhhhhhhh.eeeeeeeeee..........eeeeeeee.eee...........----.--...........eeeeeehhhhhhhhhheee......eeeeeeee...hhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhhh.......eeeee.....eeeee.........hhhhhhhhhhhhhhhhhhhhhhh...eeeee..eeeee....hhhhhhhh.......eeeeeeeeeeeeee..eeeeeeeeee....eee.......eeeeeeee...hhhhhh...........ee...eeeeee..eeeeee..ee. Sec.struct. author
                 SAPs(SNPs) ---------------------------------------------------------------------------------------------------------------------------------------------------------------------------R----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------V--------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------- SAPs(SNPs)
                    PROSITE -----------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------DNA_POLYM---------------------------------------------------------------------------------------------------------------- PROSITE
                 Transcript ------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------------ Transcript
                 2pzs D   5 PRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIK----Y--NEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTI 574
                                    14        24        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       444       454       464       474       484       494       504       514       524       534       544       554       564       574
                                                                                                                                                                                                                                                                                                                                      305  310  |                                                                                                                                                                                                                                                                     
                                                                                                                                                                                                                                                                                                                                              313

Chain R from PDB  Type:DNA  Length:10
                                          
                 2pzs R   1 GACTGCTTAC  10
                                    10

Chain S from PDB  Type:DNA  Length:14
                                              
                 2pzs S   4 ACACGTAAGCAGTC  17
                                    13

Chain T from PDB  Type:DNA  Length:5
                                     
                 2pzs T   1 ACACG   5

Chain U from PDB  Type:DNA  Length:7
                                       
                 2pzs U   1 ACACGTA   7

Chain X from PDB  Type:DNA  Length:10
                                          
                 2pzs X   1 GACTGCTTAC  10
                                    10

Chain Y from PDB  Type:DNA  Length:14
                                              
                 2pzs Y   4 ACACGTAAGCAGTC  17
                                    13

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: Alpha and beta proteins (a/b) (23833)

Fold: Ribonuclease H-like motif (1424)

Superfamily: Ribonuclease H-like (775)

Family: DnaQ-like 3'-5' exonuclease (253)

Protein domain: Exonuclease domain of phi29 DNA polymerase (8)

Bacteriophage phi-29 [TaxId: 10756] (8)

1a	d2pzsa1	A:5-187
1b	d2pzsb1	B:5-187
1c	d2pzsc1	C:5-187
1d	d2pzsd1	D:5-187

Class: Multi-domain proteins (alpha and beta) (2421)

Fold: DNA/RNA polymerases (850)

Superfamily: DNA/RNA polymerases (850)

Family: DNA polymerase I (233)

Protein domain: phi29 DNA polymerase (8)

Bacteriophage phi-29 [TaxId: 10756] (8)

2a	d2pzsa2	A:188-575
2b	d2pzsb2	B:188-575
2c	d2pzsc2	C:188-575
2d	d2pzsd2	D:188-574

Asymmetric Unit

Classes(

)

Architectures( (-)

)

Topologies( (-)

)

Homologous Superfamilies( (-)

)

Organisms( (-)

)

Class: Alpha Beta (26913)

Architecture: 2-Layer Sandwich (8480)

Topology: Nucleotidyltransferase; domain 5 (788)

Homologous Superfamily: [code=3.30.420.10, no name defined] (372)

[unclassified] (102)

1a	2pzsA01	A:5-188
1b	2pzsD01	D:5-188
1c	2pzsB01	B:5-188
1d	2pzsC01	C:5-188

Topology: TPR 1 domain of DNA polymerase (8)

Homologous Superfamily: TPR 1 domain of DNA polymerase (8)

[unclassified] (6)

2a	2pzsA03	A:262-359
2b	2pzsD03	D:262-359
2c	2pzsC03	C:262-359
2d	2pzsB03	B:262-359

Architecture: Alpha-Beta Complex (3881)

Topology: Palm domain of DNA polymerase (8)

Homologous Superfamily: Palm domain of DNA polymerase (8)

[unclassified] (6)

3a	2pzsA02	A:189-261,A:426-531
3b	2pzsD02	D:189-261,D:426-531
3c	2pzsB02	B:189-261,B:426-531
3d	2pzsC02	C:189-261,C:426-531

Class: Few Secondary Structures (1120)

Architecture: Irregular (1120)

Topology: Rhinovirus 14, subunit 4 (101)

Homologous Superfamily: DNA polymerase; domain 5 (8)

[unclassified] (6)

4a	2pzsA05	A:396-425
4b	2pzsD05	D:396-425
4c	2pzsB05	B:396-425
4d	2pzsC05	C:396-425

Homologous Superfamily: DNA polymerase; domain 6 (10)

[unclassified] (6)

5a	2pzsD06	D:532-574
5b	2pzsC06	C:532-575
5c	2pzsA06	A:532-575
5d	2pzsB06	B:532-575

Class: Mainly Alpha (13335)

Architecture: Orthogonal Bundle (10391)

Topology: Helix Hairpins (718)

Homologous Superfamily: Helix hairpin bin (10)

[unclassified] (7)

6a	2pzsA04	A:360-395
6b	2pzsD04	D:360-395
6c	2pzsB04	B:360-395
6d	2pzsC04	C:360-395

Asymmetric Unit

Clans(

)

Families(

)

Organisms( (-)

)

Clan: DNA_pol_B-like (44)

Family: DNA_pol_B_2 (6)

Bacillus phage phi29 (Bacteriophage phi-29) (6)

1a	DNA_pol_B_2-2pzsD01	D:49-488
1b	DNA_pol_B_2-2pzsD02	D:49-488
1c	DNA_pol_B_2-2pzsD03	D:49-488
1d	DNA_pol_B_2-2pzsD04	D:49-488

Asymmetric Unit(hide GO term definitions)

Chain A,B,C,D (DPOL_BPPH2 | P03680)

molecular function
	GO:0008408	3'-5' exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' end.
	GO:0003677	DNA binding	Any molecular function by which a gene product interacts selectively and non-covalently with DNA (deoxyribonucleic acid).
	GO:0003887	DNA-directed DNA polymerase activity	Catalysis of the reaction: deoxynucleoside triphosphate + DNA(n) = diphosphate + DNA(n+1); the synthesis of DNA from deoxyribonucleotide triphosphates in the presence of a DNA template and a 3'hydroxyl group.
	GO:0004527	exonuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids by removing nucleotide residues from the 3' or 5' end.
	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:0004518	nuclease activity	Catalysis of the hydrolysis of ester linkages within nucleic acids.
	GO:0003676	nucleic acid binding	Interacting selectively and non-covalently with any nucleic acid.
	GO:0001882	nucleoside binding	Interacting selectively and non-covalently with a nucleoside, a compound consisting of a purine or pyrimidine nitrogenous base linked either to ribose or deoxyribose.
	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:0016779	nucleotidyltransferase activity	Catalysis of the transfer of a nucleotidyl group to a reactant.
	GO:0016740	transferase activity	Catalysis of the transfer of a group, e.g. a methyl group, glycosyl group, acyl group, phosphorus-containing, or other groups, from one compound (generally regarded as the donor) to another compound (generally regarded as the acceptor). Transferase is the systematic name for any enzyme of EC class 2.
biological process
	GO:0071897	DNA biosynthetic process	The cellular DNA metabolic process resulting in the formation of DNA, deoxyribonucleic acid, one of the two main types of nucleic acid, consisting of a long unbranched macromolecule formed from one or two strands of linked deoxyribonucleotides, the 3'-phosphate group of each constituent deoxyribonucleotide being joined in 3',5'-phosphodiester linkage to the 5'-hydroxyl group of the deoxyribose moiety of the next one.
	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:0090305	nucleic acid phosphodiester bond hydrolysis	The nucleic acid metabolic process in which the phosphodiester bonds between nucleotides are cleaved by hydrolysis.
	GO:0039693	viral DNA genome replication	The replication of a viral DNA genome.

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
(no "Ligands, Modified Residues, Ions" information available for 2pzs)

	Sites
(no "Sites" information available for 2pzs)

	Cis Peptide Bonds
		Phe C:292 - Glu C:293	[ RasMol ]

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 \| Biol. Unit 1 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
	2pzs
		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
	DPOL_BPPH2 \| P03680
		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)
	2.7.7.7
		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
	DPOL_BPPH2 \| P03680
		Protein Disorder Prediction	:	DisEMBL \| FoldIndex \| GLOBPLOT (for more information see DisProt)

UniProtKB/Swiss-Prot
	DPOL_BPPH2 \| P03680	:	1xhx 1xhz 1xi1 2ex3 2py5 2pyj 2pyl

2py5	PHI29 DNA POLYMERASE COMPLEXED WITH SINGLE-STRANDED DNA
2pyj	PHI29 DNA POLYMERASE COMPLEXED WITH PRIMER-TEMPLATE SUBSTRATE (POST-TRANSLOCATED BINARY COMPLEX)
2pyl	PHI29 DNA POLYMERASE COMPLEXED WITH PRIMER-TEMPLATE AND INCOMING NUCLEOTIDE SUBSTRATES (PRE-TRANSLOCATED TERNARY COMPLEX)

Description

Compounds

Structural Features

Chains, Units

Ligands, Modified Residues, Ions (0, 0)

Sites (0, 0)

SS Bonds (0, 0)

Cis Peptide Bonds (1, 1)

Sequence-Structure Mapping

SAPs(SNPs)/Variants (2, 8)

PROSITE Motifs (1, 4)

Exons (0, 0)

Sequences/Alignments

Classification and Annotation

SCOP Domains (2, 8)

CATH Domains (6, 24)

Pfam Domains (1, 4)

Gene Ontology (16, 16)

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