Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2EX3

Bacteriophage phi29 DNA polymerase bound to terminal protein

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0001882	molecular_function	nucleoside binding
A	0003676	molecular_function	nucleic acid binding
A	0003677	molecular_function	DNA binding
A	0003887	molecular_function	DNA-directed DNA polymerase activity
A	0004518	molecular_function	nuclease activity
A	0004527	molecular_function	exonuclease activity
A	0006260	biological_process	DNA replication
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016787	molecular_function	hydrolase activity
A	0034061	molecular_function	DNA polymerase activity
A	0039693	biological_process	viral DNA genome replication
A	0046872	molecular_function	metal ion binding
B	0006260	biological_process	DNA replication
B	0006269	biological_process	DNA replication, synthesis of primer
C	0000166	molecular_function	nucleotide binding
C	0001882	molecular_function	nucleoside binding
C	0003676	molecular_function	nucleic acid binding
C	0003677	molecular_function	DNA binding
C	0003887	molecular_function	DNA-directed DNA polymerase activity
C	0004518	molecular_function	nuclease activity
C	0004527	molecular_function	exonuclease activity
C	0006260	biological_process	DNA replication
C	0016740	molecular_function	transferase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0016787	molecular_function	hydrolase activity
C	0034061	molecular_function	DNA polymerase activity
C	0039693	biological_process	viral DNA genome replication
C	0046872	molecular_function	metal ion binding
D	0006260	biological_process	DNA replication
D	0006269	biological_process	DNA replication, synthesis of primer
E	0000166	molecular_function	nucleotide binding
E	0001882	molecular_function	nucleoside binding
E	0003676	molecular_function	nucleic acid binding
E	0003677	molecular_function	DNA binding
E	0003887	molecular_function	DNA-directed DNA polymerase activity
E	0004518	molecular_function	nuclease activity
E	0004527	molecular_function	exonuclease activity
E	0006260	biological_process	DNA replication
E	0016740	molecular_function	transferase activity
E	0016779	molecular_function	nucleotidyltransferase activity
E	0016787	molecular_function	hydrolase activity
E	0034061	molecular_function	DNA polymerase activity
E	0039693	biological_process	viral DNA genome replication
E	0046872	molecular_function	metal ion binding
F	0006260	biological_process	DNA replication
F	0006269	biological_process	DNA replication, synthesis of primer
G	0000166	molecular_function	nucleotide binding
G	0001882	molecular_function	nucleoside binding
G	0003676	molecular_function	nucleic acid binding
G	0003677	molecular_function	DNA binding
G	0003887	molecular_function	DNA-directed DNA polymerase activity
G	0004518	molecular_function	nuclease activity
G	0004527	molecular_function	exonuclease activity
G	0006260	biological_process	DNA replication
G	0016740	molecular_function	transferase activity
G	0016779	molecular_function	nucleotidyltransferase activity
G	0016787	molecular_function	hydrolase activity
G	0034061	molecular_function	DNA polymerase activity
G	0039693	biological_process	viral DNA genome replication
G	0046872	molecular_function	metal ion binding
H	0006260	biological_process	DNA replication
H	0006269	biological_process	DNA replication, synthesis of primer
I	0000166	molecular_function	nucleotide binding
I	0001882	molecular_function	nucleoside binding
I	0003676	molecular_function	nucleic acid binding
I	0003677	molecular_function	DNA binding
I	0003887	molecular_function	DNA-directed DNA polymerase activity
I	0004518	molecular_function	nuclease activity
I	0004527	molecular_function	exonuclease activity
I	0006260	biological_process	DNA replication
I	0016740	molecular_function	transferase activity
I	0016779	molecular_function	nucleotidyltransferase activity
I	0016787	molecular_function	hydrolase activity
I	0034061	molecular_function	DNA polymerase activity
I	0039693	biological_process	viral DNA genome replication
I	0046872	molecular_function	metal ion binding
J	0006260	biological_process	DNA replication
J	0006269	biological_process	DNA replication, synthesis of primer
K	0000166	molecular_function	nucleotide binding
K	0001882	molecular_function	nucleoside binding
K	0003676	molecular_function	nucleic acid binding
K	0003677	molecular_function	DNA binding
K	0003887	molecular_function	DNA-directed DNA polymerase activity
K	0004518	molecular_function	nuclease activity
K	0004527	molecular_function	exonuclease activity
K	0006260	biological_process	DNA replication
K	0016740	molecular_function	transferase activity
K	0016779	molecular_function	nucleotidyltransferase activity
K	0016787	molecular_function	hydrolase activity
K	0034061	molecular_function	DNA polymerase activity
K	0039693	biological_process	viral DNA genome replication
K	0046872	molecular_function	metal ion binding
L	0006260	biological_process	DNA replication
L	0006269	biological_process	DNA replication, synthesis of primer

Functional Information from PDB Data

site_id	AC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB A 701

Chain	Residue
A	ASP169

site_id	AC2
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PB A 702

Chain	Residue
A	GLU14
A	ASP145
A	TYR148
A	ASP169

site_id	AC3
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB A 703

Chain	Residue
A	GLU221

site_id	AC4
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB C 704

Chain	Residue
C	ASP169

site_id	AC5
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PB C 705

Chain	Residue
C	GLU14
C	ASP169

site_id	AC6
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PB E 707

Chain	Residue
E	GLU14
E	ASP169

site_id	AC7
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB E 708

Chain	Residue
E	ASP169

site_id	AC8
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB G 710

Chain	Residue
G	ASP169

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE PB G 711

Chain	Residue
G	GLU14
G	ASP145
G	TYR148
G	ASP169

site_id	BC1
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB G 712

Chain	Residue
G	GLU221

site_id	BC2
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB I 713

Chain	Residue
I	ASP169

site_id	BC3
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PB I 714

Chain	Residue
I	GLU14
I	ASP169

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE PB K 715

Chain	Residue
K	GLU14
K	ASP169

site_id	BC5
Number of Residues	1
Details	BINDING SITE FOR RESIDUE PB K 716

Chain	Residue
K	ASP169

Functional Information from PROSITE/UniProt

site_id	PS00116
Number of Residues	9
Details	DNA_POLYMERASE_B DNA polymerase family B signature. YCDTDSIHL

Chain	Residue	Details
A	TYR454-LEU462

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	222
Details	Region: {"description":"Involved in DNA-binding, coordination between DNA synthesis and degradation and TP interaction","evidences":[{"source":"PubMed","id":"15777661","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8670845","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9931249","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI2
Number of Residues	1992
Details	Region: {"description":"Initiation, polymerization and pyrophosphorolytic activities","evidences":[{"source":"PubMed","id":"8621470","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	132
Details	Region: {"description":"TPR2","evidences":[{"source":"PubMed","id":"15845765","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	72
Details	Region: {"description":"Involved in DNA-binding and TP interaction","evidences":[{"source":"PubMed","id":"14729920","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	24
Details	Motif: {"description":"YCDTD","evidences":[{"source":"PubMed","id":"1850426","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	12
Details	Binding site: {"evidences":[{"source":"PDB","id":"1XI1","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"8226957","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2PYJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI8
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"19883660","evidenceCode":"ECO:0000269"},{"source":"PDB","id":"2PYJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	18
Details	Binding site: {"evidences":[{"source":"PDB","id":"2PYL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PubMed","id":"9784372","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PDB","id":"2PYJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	18
Details	Site: {"description":"Essential for 3'-5' exonucleolysis","evidences":[{"source":"PubMed","id":"2790959","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"8344956","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI13
Number of Residues	12
Details	Site: {"description":"Involved in proofreading function by stabilization of the frayed primer-terminus at the 3'-5' exonuclease active site","evidences":[{"source":"PubMed","id":"8605889","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	18
Details	Site: {"description":"Interaction with the primer terminal protein","evidences":[{"source":"PubMed","id":"11884636","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI15
Number of Residues	18
Details	Site: {"description":"Binds ssDNA; Essential for 3'-5' exonucleolysis","evidences":[{"source":"PubMed","id":"9786901","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	6
Details	Site: {"description":"Involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"8344956","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI17
Number of Residues	6
Details	Site: {"description":"Involved in the stabilization of the frayed 3' terminus at the exonuclease active site","evidences":[{"source":"PubMed","id":"19576228","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI18
Number of Residues	6
Details	Site: {"description":"Probably involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"8226957","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	12
Details	Site: {"description":"Probably involved in nucleotide binding selection","evidences":[{"source":"PubMed","id":"8537389","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI20
Number of Residues	12
Details	Site: {"description":"Binds ssDNA; Essential for 3'-5' exonucleolysis","evidences":[{"source":"PubMed","id":"8605889","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI21
Number of Residues	6
Details	Site: {"description":"Involved in the binding of DNA and dNTP","evidences":[{"source":"PubMed","id":"11917008","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	12
Details	Site: {"description":"Stabilization of the incoming nucleotide","evidences":[{"source":"PubMed","id":"14672657","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI23
Number of Residues	6
Details	Site: {"description":"Interacts with the phosphate groups of the incoming nucleotide","evidences":[{"source":"PubMed","id":"11917008","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
Number of Residues	6
Details	Site: {"description":"Probably involved in nucleotide binding selection","evidences":[{"source":"PubMed","id":"9199402","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI25
Number of Residues	6
Details	Site: {"description":"Probably involved in positioning the templating nucleotide at the polymerization active site and in controlling nucleotide insertion fidelity","evidences":[{"source":"PubMed","id":"12805385","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI26
Number of Residues	12
Details	Site: {"description":"Probably involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"8344956","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI27
Number of Residues	12
Details	Site: {"description":"Probably involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"7962004","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI28
Number of Residues	12
Details	Site: {"description":"Probably involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"7852344","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI29
Number of Residues	6
Details	Site: {"description":"Stabilizes the primer-terminus at the polymerization active site and contributes to the coordination between the exonuclease and polymerazation activities","evidences":[{"source":"PubMed","id":"24023769","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)
		EDMap 2fo-fc (MTZ)