Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6N9X

Structure of bacteriophage T7 lagging-strand DNA polymerase (D5A/E7A) and gp4 (helicase/primase) bound to DNA including RNA/DNA hybrid, and an incoming dTTP (LagS3)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0003677	molecular_function	DNA binding
A	0003678	molecular_function	DNA helicase activity
A	0003689	molecular_function	DNA clamp loader activity
A	0003697	molecular_function	single-stranded DNA binding
A	0003896	molecular_function	DNA primase activity
A	0004386	molecular_function	helicase activity
A	0005515	molecular_function	protein binding
A	0005524	molecular_function	ATP binding
A	0006260	biological_process	DNA replication
A	0006269	biological_process	DNA replication, synthesis of primer
A	0006338	biological_process	chromatin remodeling
A	0008270	molecular_function	zinc ion binding
A	0009378	molecular_function	four-way junction helicase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016787	molecular_function	hydrolase activity
A	0016887	molecular_function	ATP hydrolysis activity
A	0032508	biological_process	DNA duplex unwinding
A	0036121	molecular_function	double-stranded DNA helicase activity
A	0039693	biological_process	viral DNA genome replication
A	0042802	molecular_function	identical protein binding
A	0043139	molecular_function	5'-3' DNA helicase activity
A	0046872	molecular_function	metal ion binding
A	0061749	molecular_function	forked DNA-dependent helicase activity
A	0061775	molecular_function	cohesin loader activity
A	0140584	molecular_function	chromatin extrusion motor activity
A	0140588	biological_process	chromatin looping
A	0140665	molecular_function	ATP-dependent H3-H4 histone complex chaperone activity
A	0140849	molecular_function	ATP-dependent H2AZ histone chaperone activity
A	1990518	molecular_function	single-stranded 3'-5' DNA helicase activity
B	0003677	molecular_function	DNA binding
B	0003678	molecular_function	DNA helicase activity
B	0003689	molecular_function	DNA clamp loader activity
B	0003697	molecular_function	single-stranded DNA binding
B	0003896	molecular_function	DNA primase activity
B	0004386	molecular_function	helicase activity
B	0005515	molecular_function	protein binding
B	0005524	molecular_function	ATP binding
B	0006260	biological_process	DNA replication
B	0006269	biological_process	DNA replication, synthesis of primer
B	0006338	biological_process	chromatin remodeling
B	0008270	molecular_function	zinc ion binding
B	0009378	molecular_function	four-way junction helicase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0016787	molecular_function	hydrolase activity
B	0016887	molecular_function	ATP hydrolysis activity
B	0032508	biological_process	DNA duplex unwinding
B	0036121	molecular_function	double-stranded DNA helicase activity
B	0039693	biological_process	viral DNA genome replication
B	0042802	molecular_function	identical protein binding
B	0043139	molecular_function	5'-3' DNA helicase activity
B	0046872	molecular_function	metal ion binding
B	0061749	molecular_function	forked DNA-dependent helicase activity
B	0061775	molecular_function	cohesin loader activity
B	0140584	molecular_function	chromatin extrusion motor activity
B	0140588	biological_process	chromatin looping
B	0140665	molecular_function	ATP-dependent H3-H4 histone complex chaperone activity
B	0140849	molecular_function	ATP-dependent H2AZ histone chaperone activity
B	1990518	molecular_function	single-stranded 3'-5' DNA helicase activity
C	0003677	molecular_function	DNA binding
C	0003678	molecular_function	DNA helicase activity
C	0003689	molecular_function	DNA clamp loader activity
C	0003697	molecular_function	single-stranded DNA binding
C	0003896	molecular_function	DNA primase activity
C	0004386	molecular_function	helicase activity
C	0005515	molecular_function	protein binding
C	0005524	molecular_function	ATP binding
C	0006260	biological_process	DNA replication
C	0006269	biological_process	DNA replication, synthesis of primer
C	0006338	biological_process	chromatin remodeling
C	0008270	molecular_function	zinc ion binding
C	0009378	molecular_function	four-way junction helicase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0016787	molecular_function	hydrolase activity
C	0016887	molecular_function	ATP hydrolysis activity
C	0032508	biological_process	DNA duplex unwinding
C	0036121	molecular_function	double-stranded DNA helicase activity
C	0039693	biological_process	viral DNA genome replication
C	0042802	molecular_function	identical protein binding
C	0043139	molecular_function	5'-3' DNA helicase activity
C	0046872	molecular_function	metal ion binding
C	0061749	molecular_function	forked DNA-dependent helicase activity
C	0061775	molecular_function	cohesin loader activity
C	0140584	molecular_function	chromatin extrusion motor activity
C	0140588	biological_process	chromatin looping
C	0140665	molecular_function	ATP-dependent H3-H4 histone complex chaperone activity
C	0140849	molecular_function	ATP-dependent H2AZ histone chaperone activity
C	1990518	molecular_function	single-stranded 3'-5' DNA helicase activity
D	0003677	molecular_function	DNA binding
D	0003678	molecular_function	DNA helicase activity
D	0003689	molecular_function	DNA clamp loader activity
D	0003697	molecular_function	single-stranded DNA binding
D	0003896	molecular_function	DNA primase activity
D	0004386	molecular_function	helicase activity
D	0005515	molecular_function	protein binding
D	0005524	molecular_function	ATP binding
D	0006260	biological_process	DNA replication
D	0006269	biological_process	DNA replication, synthesis of primer
D	0006338	biological_process	chromatin remodeling
D	0008270	molecular_function	zinc ion binding
D	0009378	molecular_function	four-way junction helicase activity
D	0016779	molecular_function	nucleotidyltransferase activity
D	0016787	molecular_function	hydrolase activity
D	0016887	molecular_function	ATP hydrolysis activity
D	0032508	biological_process	DNA duplex unwinding
D	0036121	molecular_function	double-stranded DNA helicase activity
D	0039693	biological_process	viral DNA genome replication
D	0042802	molecular_function	identical protein binding
D	0043139	molecular_function	5'-3' DNA helicase activity
D	0046872	molecular_function	metal ion binding
D	0061749	molecular_function	forked DNA-dependent helicase activity
D	0061775	molecular_function	cohesin loader activity
D	0140584	molecular_function	chromatin extrusion motor activity
D	0140588	biological_process	chromatin looping
D	0140665	molecular_function	ATP-dependent H3-H4 histone complex chaperone activity
D	0140849	molecular_function	ATP-dependent H2AZ histone chaperone activity
D	1990518	molecular_function	single-stranded 3'-5' DNA helicase activity
E	0003677	molecular_function	DNA binding
E	0003678	molecular_function	DNA helicase activity
E	0003689	molecular_function	DNA clamp loader activity
E	0003697	molecular_function	single-stranded DNA binding
E	0003896	molecular_function	DNA primase activity
E	0004386	molecular_function	helicase activity
E	0005515	molecular_function	protein binding
E	0005524	molecular_function	ATP binding
E	0006260	biological_process	DNA replication
E	0006269	biological_process	DNA replication, synthesis of primer
E	0006338	biological_process	chromatin remodeling
E	0008270	molecular_function	zinc ion binding
E	0009378	molecular_function	four-way junction helicase activity
E	0016779	molecular_function	nucleotidyltransferase activity
E	0016787	molecular_function	hydrolase activity
E	0016887	molecular_function	ATP hydrolysis activity
E	0032508	biological_process	DNA duplex unwinding
E	0036121	molecular_function	double-stranded DNA helicase activity
E	0039693	biological_process	viral DNA genome replication
E	0042802	molecular_function	identical protein binding
E	0043139	molecular_function	5'-3' DNA helicase activity
E	0046872	molecular_function	metal ion binding
E	0061749	molecular_function	forked DNA-dependent helicase activity
E	0061775	molecular_function	cohesin loader activity
E	0140584	molecular_function	chromatin extrusion motor activity
E	0140588	biological_process	chromatin looping
E	0140665	molecular_function	ATP-dependent H3-H4 histone complex chaperone activity
E	0140849	molecular_function	ATP-dependent H2AZ histone chaperone activity
E	1990518	molecular_function	single-stranded 3'-5' DNA helicase activity
F	0003677	molecular_function	DNA binding
F	0003678	molecular_function	DNA helicase activity
F	0003689	molecular_function	DNA clamp loader activity
F	0003697	molecular_function	single-stranded DNA binding
F	0003896	molecular_function	DNA primase activity
F	0004386	molecular_function	helicase activity
F	0005515	molecular_function	protein binding
F	0005524	molecular_function	ATP binding
F	0006260	biological_process	DNA replication
F	0006269	biological_process	DNA replication, synthesis of primer
F	0006338	biological_process	chromatin remodeling
F	0008270	molecular_function	zinc ion binding
F	0009378	molecular_function	four-way junction helicase activity
F	0016779	molecular_function	nucleotidyltransferase activity
F	0016787	molecular_function	hydrolase activity
F	0016887	molecular_function	ATP hydrolysis activity
F	0032508	biological_process	DNA duplex unwinding
F	0036121	molecular_function	double-stranded DNA helicase activity
F	0039693	biological_process	viral DNA genome replication
F	0042802	molecular_function	identical protein binding
F	0043139	molecular_function	5'-3' DNA helicase activity
F	0046872	molecular_function	metal ion binding
F	0061749	molecular_function	forked DNA-dependent helicase activity
F	0061775	molecular_function	cohesin loader activity
F	0140584	molecular_function	chromatin extrusion motor activity
F	0140588	biological_process	chromatin looping
F	0140665	molecular_function	ATP-dependent H3-H4 histone complex chaperone activity
F	0140849	molecular_function	ATP-dependent H2AZ histone chaperone activity
F	1990518	molecular_function	single-stranded 3'-5' DNA helicase activity
H	0000166	molecular_function	nucleotide binding
H	0003676	molecular_function	nucleic acid binding
H	0003677	molecular_function	DNA binding
H	0003887	molecular_function	DNA-directed DNA polymerase activity
H	0004527	molecular_function	exonuclease activity
H	0004529	molecular_function	DNA exonuclease activity
H	0005515	molecular_function	protein binding
H	0006259	biological_process	DNA metabolic process
H	0006260	biological_process	DNA replication
H	0006261	biological_process	DNA-templated DNA replication
H	0006302	biological_process	double-strand break repair
H	0008408	molecular_function	3'-5' exonuclease activity
H	0034061	molecular_function	DNA polymerase activity
H	0039693	biological_process	viral DNA genome replication
H	0046872	molecular_function	metal ion binding
H	0090592	biological_process	DNA synthesis involved in DNA replication

Functional Information from PDB Data

site_id	AC1
Number of Residues	4
Details	binding site for residue ZN B 601

Chain	Residue
B	CYS17
B	CYS20
B	CYS36
B	CYS39

site_id	AC2
Number of Residues	15
Details	binding site for residue TTP B 602

Chain	Residue
B	GLY317
B	LYS318
B	SER319
B	THR320
B	GLN343
B	HIS465
B	ARG504
B	ASN512
B	TYR535
B	MG603
A	LYS520
A	ARG522
A	GLY525
B	GLY315
B	MET316

site_id	AC3
Number of Residues	3
Details	binding site for residue MG B 603

Chain	Residue
B	SER319
B	GLN343
B	TTP602

site_id	AC4
Number of Residues	18
Details	binding site for residue TTP C 700

Chain	Residue
B	ARG522
B	PHE523
B	THR524
B	GLY525
C	GLY315
C	MET316
C	GLY317
C	LYS318
C	SER319
C	THR320
C	GLN343
C	ARG361
C	HIS465
C	ARG504
C	ASN512
C	TYR535
C	LYS537
C	MG701

site_id	AC5
Number of Residues	3
Details	binding site for residue MG C 701

Chain	Residue
C	SER319
C	GLN343
C	TTP700

site_id	AC6
Number of Residues	17
Details	binding site for residue TTP D 700

Chain	Residue
C	GLN494
C	ARG522
C	PHE523
C	THR524
C	GLY525
D	GLY315
D	MET316
D	GLY317
D	LYS318
D	SER319
D	THR320
D	GLN343
D	HIS465
D	ARG504
D	ASN512
D	TYR535
D	MG701

site_id	AC7
Number of Residues	3
Details	binding site for residue MG D 701

Chain	Residue
D	SER319
D	GLN343
D	TTP700

site_id	AC8
Number of Residues	14
Details	binding site for residue TTP E 700

Chain	Residue
D	GLN494
D	LYS520
D	CYS521
D	ARG522
E	MET316
E	GLY317
E	LYS318
E	SER319
E	THR320
E	GLN343
E	ASN512
E	TYR535
E	LYS537
E	MG701

site_id	AC9
Number of Residues	3
Details	binding site for residue MG E 701

Chain	Residue
E	SER319
E	GLN343
E	TTP700

site_id	AD1
Number of Residues	14
Details	binding site for residue TTP H 801

Chain	Residue
H	ASP475
H	ALA476
H	GLY478
H	LEU479
H	GLU480
H	HIS506
H	ARG518
H	LYS522
H	TYR526
H	ASP654
H	MG802
P	DOC6
T	DA2004
T	DG2005

site_id	AD2
Number of Residues	4
Details	binding site for residue MG H 802

Chain	Residue
H	ASP475
H	ALA476
H	ASP654
H	TTP801

site_id	AD3
Number of Residues	1
Details	binding site for residue MG H 803

Chain	Residue
H	HIS59

Functional Information from PROSITE/UniProt

site_id	PS00447
Number of Residues	20
Details	DNA_POLYMERASE_A DNA polymerase family A signature. RdnAKtfiYGflYgaGdekI

Chain	Residue	Details
H	ARG518-ILE537

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	3
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_04101, ECO:0000305\|PubMed:9440688

Chain	Residue	Details
H	ALA5
H	ALA7
H	ASP174
D	CYS17-CYS39
E	CYS17-CYS39
F	CYS17-CYS39

site_id	SWS_FT_FI2
Number of Residues	3
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_04101, ECO:0000269\|PubMed:9440688, ECO:0000305\|PubMed:9914251

Chain	Residue	Details
H	ASP475
B	ASP237
C	CYS17
C	CYS20
C	CYS36
C	CYS39
C	ASP237
D	CYS17
D	CYS20
D	CYS36
D	CYS39
H	ALA476
D	ASP237
E	CYS17
E	CYS20
E	CYS36
E	CYS39
E	ASP237
F	CYS17
F	CYS20
F	CYS36
F	CYS39
H	ASP654
F	ASP237
A	CYS39
A	ASP237
B	CYS17
B	CYS20
B	CYS36
B	CYS39

site_id	SWS_FT_FI3
Number of Residues	4
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_04101, ECO:0000305\|PubMed:9914251

Chain	Residue	Details
H	HIS506
E	ASP207
F	GLU157
F	ASP207
H	ARG518
H	LYS522
H	TYR526
C	GLU157
C	ASP207
D	GLU157
D	ASP207
E	GLU157

site_id	SWS_FT_FI4
Number of Residues	6
Details	BINDING: BINDING => ECO:0000255\|HAMAP-Rule:MF_04154

Chain	Residue	Details
A	SER312
B	SER312
C	SER312
D	SER312
E	SER312
F	SER312

site_id	SWS_FT_FI5
Number of Residues	6
Details	SITE: dTTP/dATP binding => ECO:0000255\|HAMAP-Rule:MF_04154, ECO:0000305\|PubMed:10892646

Chain	Residue	Details
A	ARG361
B	ARG361
C	ARG361
D	ARG361
E	ARG361
F	ARG361

site_id	SWS_FT_FI6
Number of Residues	6
Details	SITE: dTTP/dATP binding => ECO:0000255\|HAMAP-Rule:MF_04154, ECO:0000305\|PubMed:10535735

Chain	Residue	Details
A	HIS465
B	HIS465
C	HIS465
D	HIS465
E	HIS465
F	HIS465

site_id	SWS_FT_FI7
Number of Residues	18
Details	SITE: dTTP/dATP binding => ECO:0000255\|HAMAP-Rule:MF_04154, ECO:0000305\|PubMed:10535735, ECO:0000305\|PubMed:10892646

Chain	Residue	Details
A	ARG504
D	ARG504
D	ARG522
D	TYR535
E	ARG504
E	ARG522
E	TYR535
F	ARG504
F	ARG522
F	TYR535
A	ARG522
A	TYR535
B	ARG504
B	ARG522
B	TYR535
C	ARG504
C	ARG522
C	TYR535

		Sequence (fasta)
		PDBx/mmCIF
		PDBML format (no-atom)
		PDB format (full)
		Validation report (PDF)