Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2PYL

Phi29 DNA polymerase complexed with primer-template DNA and incoming nucleotide substrates (ternary 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

Functional Information from PDB Data

site_id	AC1
Number of Residues	8
Details	BINDING SITE FOR RESIDUE MG A 3202

Chain	Residue
A	ASP249
A	VAL250
A	ASP458
A	MG3203
A	TTP3204
A	HOH3274
A	HOH3523
A	HOH3525

site_id	AC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE MG A 3203

Chain	Residue
A	ASP458
A	MG3202
A	TTP3204
A	HOH3525
A	ASP249

site_id	AC3
Number of Residues	21
Details	BINDING SITE FOR RESIDUE TTP A 3204

Chain	Residue
A	LEU253
A	TYR254
A	LYS371
A	LYS383
A	ASN387
A	ASP458
A	MG3202
A	MG3203
A	HOH3233
A	HOH3235
A	HOH3265
A	HOH3274
A	HOH3300
A	HOH3501
A	HOH3523
A	HOH3524
A	HOH3525
A	HOH3527
X	2DA11
Y	DA6
Y	DT7

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 1001

Chain	Residue
A	ILE158
A	GLU291
A	EDO1004

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 1002

Chain	Residue
A	GLN257
A	SER260
A	THR440
A	GLY481
A	HOH3504

site_id	AC6
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 1003

Chain	Residue
A	LYS80
A	PRO87
A	ASN88

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 1004

Chain	Residue
A	ILE40
A	ASN42
A	ILE158
A	ASN344
A	EDO1001

site_id	AC8
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 1005

Chain	Residue
A	TYR59
A	ASP186
A	ARG187
A	MET188

site_id	AC9
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 1006

Chain	Residue
A	LYS124
A	THR189
A	GLY191
A	HOH3318
Y	DA6

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	37
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	332
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	22
Details	Region: {"description":"TPR2","evidences":[{"source":"PubMed","id":"15845765","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI4
Number of Residues	12
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	4
Details	Motif: {"description":"YCDTD","evidences":[{"source":"PubMed","id":"1850426","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PDB","id":"1XI1","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI7
Number of Residues	1
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	1
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	3
Details	Binding site: {"evidences":[{"source":"PDB","id":"2PYL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PubMed","id":"9784372","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	1
Details	Binding site: {"evidences":[{"source":"PDB","id":"2PYJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI12
Number of Residues	3
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	2
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	3
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	3
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	1
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	1
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	1
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	2
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	2
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	1
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	2
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	1
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	1
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	1
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	2
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	2
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	2
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	1
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)