Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

1XHZ

Phi29 DNA polymerase, orthorhombic crystal form, ssDNA complex

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	0000166	molecular_function	nucleotide binding
B	0001882	molecular_function	nucleoside binding
B	0003676	molecular_function	nucleic acid binding
B	0003677	molecular_function	DNA binding
B	0003887	molecular_function	DNA-directed DNA polymerase activity
B	0004518	molecular_function	nuclease activity
B	0004527	molecular_function	exonuclease activity
B	0006260	biological_process	DNA replication
B	0016740	molecular_function	transferase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0016787	molecular_function	hydrolase activity
B	0034061	molecular_function	DNA polymerase activity
B	0039693	biological_process	viral DNA genome replication
B	0046872	molecular_function	metal ion binding
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	0000166	molecular_function	nucleotide binding
D	0001882	molecular_function	nucleoside binding
D	0003676	molecular_function	nucleic acid binding
D	0003677	molecular_function	DNA binding
D	0003887	molecular_function	DNA-directed DNA polymerase activity
D	0004518	molecular_function	nuclease activity
D	0004527	molecular_function	exonuclease activity
D	0006260	biological_process	DNA replication
D	0016740	molecular_function	transferase activity
D	0016779	molecular_function	nucleotidyltransferase activity
D	0016787	molecular_function	hydrolase activity
D	0034061	molecular_function	DNA polymerase activity
D	0039693	biological_process	viral DNA genome replication
D	0046872	molecular_function	metal ion binding

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	148
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	1328
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	88
Details	Region: {"description":"TPR2","evidences":[{"source":"PubMed","id":"15845765","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	48
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	16
Details	Motif: {"description":"YCDTD","evidences":[{"source":"PubMed","id":"1850426","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	8
Details	Binding site: {"evidences":[{"source":"PDB","id":"1XI1","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	4
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	4
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	12
Details	Binding site: {"evidences":[{"source":"PDB","id":"2PYL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PubMed","id":"9784372","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PDB","id":"2PYJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	12
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	8
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	12
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	12
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	4
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	4
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	4
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	8
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	8
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	4
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	8
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	4
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	4
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	4
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	8
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	8
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	8
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	4
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)