Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

2PY5

Phi29 DNA polymerase complexed with single-stranded DNA

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

Functional Information from PDB Data

site_id	AC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 8001

Chain	Residue
A	SER252
A	LYS371
A	LYS383
A	ASN387
A	HOH9362

site_id	AC2
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 8002

Chain	Residue
B	LYS238
B	GLN497
B	HOH9134

site_id	AC3
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO B 8003

Chain	Residue
B	HOH9103
B	HOH9369
B	HOH9476
B	ARG261

site_id	AC4
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 8004

Chain	Residue
A	SER260
A	THR357
A	HOH9038

site_id	AC5
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 8005

Chain	Residue
B	ILE474
B	LEU480
B	TYR482
B	HOH9084
B	HOH9273

site_id	AC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 8006

Chain	Residue
B	LEU216
B	ASP219
B	LYS220
B	ARG223
B	PRO397

site_id	AC7
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 8007

Chain	Residue
B	GLU241
B	ILE242
B	GLY243
B	ARG491
B	HOH9146

site_id	AC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 8008

Chain	Residue
A	LEU294
A	LYS295
A	GLU296
A	GLY297
A	TYR298
A	LYS317
A	TYR449

site_id	AC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 8009

Chain	Residue
A	ASN234
A	ARG236
A	TYR449
A	HOH9573

site_id	BC1
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 8010

Chain	Residue
A	LYS490
A	ARG491
A	HOH9164

site_id	BC2
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 8011

Chain	Residue
A	LYS208
A	PHE211
A	THR213
A	HOH9143
A	HOH9515
A	HOH9558

site_id	BC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 8012

Chain	Residue
A	TYR259
A	ASP365
A	THR368
A	LEU480
A	HOH9177
A	HOH9780

site_id	BC4
Number of Residues	2
Details	BINDING SITE FOR RESIDUE EDO A 8013

Chain	Residue
A	TYR405
A	ARG415

site_id	BC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 9001

Chain	Residue
A	SER43
A	ASP45
A	TRP277
A	HOH9124

site_id	BC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 9002

Chain	Residue
B	TYR259
B	ASP365
B	THR368
B	HOH9397
B	HOH9621

site_id	BC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO B 9003

Chain	Residue
B	HIS485
B	THR488
B	GLY516

site_id	BC8
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 9004

Chain	Residue
B	GLU33
B	HIS35
B	LEU178
B	LYS182
B	GLU296

site_id	BC9
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 9005

Chain	Residue
A	VAL210
A	TYR265
A	EDO9006

site_id	CC1
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 9006

Chain	Residue
A	LYS206
A	THR357
A	GLY358
A	LEU359
A	EDO9005

site_id	CC2
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 9007

Chain	Residue
A	GLU334
A	TYR439
A	HOH9126
A	HOH9753
A	HOH9773

site_id	CC3
Number of Residues	6
Details	BINDING SITE FOR RESIDUE EDO A 9008

Chain	Residue
A	GLN257
A	SER260
A	ARG261
A	THR440
A	GLY481
A	HOH9171

site_id	CC4
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO B 9009

Chain	Residue
B	VAL528
B	LYS529
B	CYS530
B	LYS538
B	HOH9446

site_id	CC5
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 9010

Chain	Residue
A	ASP456
A	THR457
A	ASP458
A	SER459

site_id	CC6
Number of Residues	5
Details	BINDING SITE FOR RESIDUE EDO A 9011

Chain	Residue
A	ILE269
A	ASP278
A	HOH9370
A	HOH9518
B	GLY111

site_id	CC7
Number of Residues	3
Details	BINDING SITE FOR RESIDUE EDO A 9012

Chain	Residue
A	HIS485
A	GLU486
A	GLY516

site_id	CC8
Number of Residues	7
Details	BINDING SITE FOR RESIDUE EDO A 9013

Chain	Residue
A	GLU338
A	THR443
A	ALA447
A	HOH9089
A	HOH9669
A	HOH9672
A	HOH9674

site_id	CC9
Number of Residues	4
Details	BINDING SITE FOR RESIDUE EDO A 9014

Chain	Residue
A	ILE504
A	GLU515
A	LYS525
A	HOH9320

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	74
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	44
Details	Region: {"description":"TPR2","evidences":[{"source":"PubMed","id":"15845765","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI3
Number of Residues	24
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_FI4
Number of Residues	8
Details	Motif: {"description":"YCDTD","evidences":[{"source":"PubMed","id":"1850426","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI5
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"PDB","id":"1XI1","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI6
Number of Residues	2
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_FI7
Number of Residues	2
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_FI8
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"PDB","id":"2PYL","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI9
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PubMed","id":"9784372","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI10
Number of Residues	2
Details	Binding site: {"evidences":[{"source":"PDB","id":"2PYJ","evidenceCode":"ECO:0007744"}]}

Chain

Residue

Details

site_id	SWS_FT_FI11
Number of Residues	6
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_FI12
Number of Residues	4
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_FI13
Number of Residues	6
Details	Site: {"description":"Interaction with the primer terminal protein","evidences":[{"source":"PubMed","id":"11884636","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI14
Number of Residues	6
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_FI15
Number of Residues	2
Details	Site: {"description":"Involved in binding template-primer structures","evidences":[{"source":"PubMed","id":"8344956","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI16
Number of Residues	2
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_FI17
Number of Residues	2
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_FI18
Number of Residues	4
Details	Site: {"description":"Probably involved in nucleotide binding selection","evidences":[{"source":"PubMed","id":"8537389","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI19
Number of Residues	4
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_FI20
Number of Residues	2
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_FI21
Number of Residues	4
Details	Site: {"description":"Stabilization of the incoming nucleotide","evidences":[{"source":"PubMed","id":"14672657","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI22
Number of Residues	2
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_FI23
Number of Residues	2
Details	Site: {"description":"Probably involved in nucleotide binding selection","evidences":[{"source":"PubMed","id":"9199402","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

site_id	SWS_FT_FI24
Number of Residues	2
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_FI25
Number of Residues	4
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_FI26
Number of Residues	4
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_FI27
Number of Residues	4
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_FI28
Number of Residues	2
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)