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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	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
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	0004527	molecular_function	exonuclease activity
B	0006260	biological_process	DNA replication
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	4
Details	BINDING: BINDING => ECO:0007744\|PDB:1XI1

Chain	Residue	Details
A	ASP145
A	ASP169
B	ASP145
B	ASP169

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

Chain	Residue	Details
A	ASP249
B	ASP249

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

Chain	Residue	Details
A	VAL250
B	VAL250

site_id	SWS_FT_FI4
Number of Residues	8
Details	BINDING: BINDING => ECO:0007744\|PDB:2PYL

Chain	Residue	Details
A	TYR254
A	LYS371
A	LYS383
A	ASP458
B	TYR254
B	LYS371
B	LYS383
B	ASP458

site_id	SWS_FT_FI5
Number of Residues	2
Details	BINDING: BINDING => ECO:0000269\|PubMed:9784372

Chain	Residue	Details
A	ASP456
B	ASP456

site_id	SWS_FT_FI6
Number of Residues	6
Details	SITE: Essential for 3'-5' exonucleolysis => ECO:0000269\|PubMed:2790959, ECO:0000269\|PubMed:8344956

Chain	Residue	Details
A	ALA12
A	GLU14
A	ALA66
B	ALA12
B	GLU14
B	ALA66

site_id	SWS_FT_FI7
Number of Residues	4
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
B	THR15
B	ASN62

site_id	SWS_FT_FI8
Number of Residues	6
Details	SITE: Interaction with the primer terminal protein => ECO:0000269\|PubMed:11884636

Chain	Residue	Details
A	TYR59
A	HIS61
A	PHE69
B	TYR59
B	HIS61
B	PHE69

site_id	SWS_FT_FI9
Number of Residues	6
Details	SITE: Binds ssDNA; Essential for 3'-5' exonucleolysis => ECO:0000269\|PubMed:9786901

Chain	Residue	Details
A	PHE65
A	SER122
A	LEU123
B	PHE65
B	SER122
B	LEU123

site_id	SWS_FT_FI10
Number of Residues	2
Details	SITE: Involved in binding template-primer structures => ECO:0000269\|PubMed:8344956

Chain	Residue	Details
A	ILE93
B	ILE93

site_id	SWS_FT_FI11
Number of Residues	2
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
B	TYR148

site_id	SWS_FT_FI12
Number of Residues	2
Details	SITE: Probably involved in binding template-primer structures => ECO:0000269\|PubMed:8226957

Chain	Residue	Details
A	SER252
B	SER252

site_id	SWS_FT_FI13
Number of Residues	4
Details	SITE: Probably involved in nucleotide binding selection => ECO:0000269\|PubMed:8537389

Chain	Residue	Details
A	TYR254
A	TYR390
B	TYR254
B	TYR390

site_id	SWS_FT_FI14
Number of Residues	4
Details	SITE: Binds ssDNA; Essential for 3'-5' exonucleolysis => ECO:0000269\|PubMed:8605889

Chain	Residue	Details
A	THR356
A	GLU420
B	THR356
B	GLU420

site_id	SWS_FT_FI15
Number of Residues	2
Details	SITE: Involved in the binding of DNA and dNTP => ECO:0000269\|PubMed:11917008

Chain	Residue	Details
A	ILE364
B	ILE364

site_id	SWS_FT_FI16
Number of Residues	4
Details	SITE: Stabilization of the incoming nucleotide => ECO:0000269\|PubMed:14672657

Chain	Residue	Details
A	LYS366
A	LYS379
B	LYS366
B	LYS379

site_id	SWS_FT_FI17
Number of Residues	2
Details	SITE: Interacts with the phosphate groups of the incoming nucleotide => ECO:0000269\|PubMed:11917008

Chain	Residue	Details
A	LYS371
B	LYS371

site_id	SWS_FT_FI18
Number of Residues	2
Details	SITE: Probably involved in nucleotide binding selection => ECO:0000269\|PubMed:9199402

Chain	Residue	Details
A	LYS383
B	LYS383

site_id	SWS_FT_FI19
Number of Residues	2
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
B	LEU384

site_id	SWS_FT_FI20
Number of Residues	4
Details	SITE: Probably involved in binding template-primer structures => ECO:0000269\|PubMed:8344956

Chain	Residue	Details
A	ASN387
A	GLY391
B	ASN387
B	GLY391

site_id	SWS_FT_FI21
Number of Residues	4
Details	SITE: Probably involved in binding template-primer structures => ECO:0000269\|PubMed:7962004

Chain	Residue	Details
A	THR434
A	ARG438
B	THR434
B	ARG438

site_id	SWS_FT_FI22
Number of Residues	4
Details	SITE: Probably involved in binding template-primer structures => ECO:0000269\|PubMed:7852344

Chain	Residue	Details
A	LYS498
A	TYR500
B	LYS498
B	TYR500

site_id	SWS_FT_FI23
Number of Residues	2
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
B	LYS529

226707

PDB entries from 2024-10-30

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