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	0004527	molecular_function	exonuclease activity
A	0006260	biological_process	DNA replication
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	2
Details	BINDING: BINDING => ECO:0007744\|PDB:1XI1

Chain	Residue	Details
A	ASP145
A	ASP169

site_id	SWS_FT_FI2
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:8226957, ECO:0007744\|PDB:2PYJ

Chain	Residue	Details
A	ASP249

site_id	SWS_FT_FI3
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:19883660, ECO:0007744\|PDB:2PYJ

Chain	Residue	Details
A	VAL250

site_id	SWS_FT_FI4
Number of Residues	4
Details	BINDING: BINDING => ECO:0007744\|PDB:2PYL

Chain	Residue	Details
A	TYR254
A	LYS371
A	LYS383
A	ASP458

site_id	SWS_FT_FI5
Number of Residues	1
Details	BINDING: BINDING => ECO:0000269\|PubMed:9784372

Chain	Residue	Details
A	ASP456

site_id	SWS_FT_FI6
Number of Residues	3
Details	SITE: Essential for 3'-5' exonucleolysis => ECO:0000269\|PubMed:2790959, ECO:0000269\|PubMed:8344956

Chain	Residue	Details
A	ALA12
A	GLU14
A	ALA66

site_id	SWS_FT_FI7
Number of Residues	2
Details	SITE: Involved in proofreading function by stabilization of the frayed primer-terminus at the 3'-5' exonuclease active site => ECO:0000269\|PubMed:8605889

Chain	Residue	Details
A	THR15
A	ASN62

site_id	SWS_FT_FI8
Number of Residues	3
Details	SITE: Interaction with the primer terminal protein => ECO:0000269\|PubMed:11884636

Chain	Residue	Details
A	TYR59
A	HIS61
A	PHE69

site_id	SWS_FT_FI9
Number of Residues	3
Details	SITE: Binds ssDNA; Essential for 3'-5' exonucleolysis => ECO:0000269\|PubMed:9786901

Chain	Residue	Details
A	PHE65
A	SER122
A	LEU123

site_id	SWS_FT_FI10
Number of Residues	1
Details	SITE: Involved in binding template-primer structures => ECO:0000269\|PubMed:8344956

Chain	Residue	Details
A	ILE93

site_id	SWS_FT_FI11
Number of Residues	1
Details	SITE: Involved in the stabilization of the frayed 3' terminus at the exonuclease active site => ECO:0000269\|PubMed:19576228

Chain	Residue	Details
A	TYR148

site_id	SWS_FT_FI12
Number of Residues	1
Details	SITE: Probably involved in binding template-primer structures => ECO:0000269\|PubMed:8226957

Chain	Residue	Details
A	SER252

site_id	SWS_FT_FI13
Number of Residues	2
Details	SITE: Probably involved in nucleotide binding selection => ECO:0000269\|PubMed:8537389

Chain	Residue	Details
A	TYR254
A	TYR390

site_id	SWS_FT_FI14
Number of Residues	2
Details	SITE: Binds ssDNA; Essential for 3'-5' exonucleolysis => ECO:0000269\|PubMed:8605889

Chain	Residue	Details
A	THR356
A	GLU420

site_id	SWS_FT_FI15
Number of Residues	1
Details	SITE: Involved in the binding of DNA and dNTP => ECO:0000269\|PubMed:11917008

Chain	Residue	Details
A	ILE364

site_id	SWS_FT_FI16
Number of Residues	2
Details	SITE: Stabilization of the incoming nucleotide => ECO:0000269\|PubMed:14672657

Chain	Residue	Details
A	LYS366
A	LYS379

site_id	SWS_FT_FI17
Number of Residues	1
Details	SITE: Interacts with the phosphate groups of the incoming nucleotide => ECO:0000269\|PubMed:11917008

Chain	Residue	Details
A	LYS371

site_id	SWS_FT_FI18
Number of Residues	1
Details	SITE: Probably involved in nucleotide binding selection => ECO:0000269\|PubMed:9199402

Chain	Residue	Details
A	LYS383

site_id	SWS_FT_FI19
Number of Residues	1
Details	SITE: Probably involved in positioning the templating nucleotide at the polymerization active site and in controlling nucleotide insertion fidelity => ECO:0000269\|PubMed:12805385

Chain	Residue	Details
A	LEU384

site_id	SWS_FT_FI20
Number of Residues	2
Details	SITE: Probably involved in binding template-primer structures => ECO:0000269\|PubMed:8344956

Chain	Residue	Details
A	ASN387
A	GLY391

site_id	SWS_FT_FI21
Number of Residues	2
Details	SITE: Probably involved in binding template-primer structures => ECO:0000269\|PubMed:7962004

Chain	Residue	Details
A	THR434
A	ARG438

site_id	SWS_FT_FI22
Number of Residues	2
Details	SITE: Probably involved in binding template-primer structures => ECO:0000269\|PubMed:7852344

Chain	Residue	Details
A	LYS498
A	TYR500

site_id	SWS_FT_FI23
Number of Residues	1
Details	SITE: Stabilizes the primer-terminus at the polymerization active site and contributes to the coordination between the exonuclease and polymerazation activities => ECO:0000269\|PubMed:24023769

Chain	Residue	Details
A	LYS529

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