6N9V

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 (LagS1)

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003677	molecular_function	DNA binding
A	0003678	molecular_function	DNA helicase activity
A	0003697	molecular_function	single-stranded DNA binding
A	0003824	molecular_function	catalytic activity
A	0003899	molecular_function	DNA-directed RNA polymerase 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	0008270	molecular_function	zinc ion binding
A	0016740	molecular_function	transferase activity
A	0016779	molecular_function	nucleotidyltransferase activity
A	0016787	molecular_function	hydrolase activity
A	0016853	molecular_function	isomerase activity
A	0016887	molecular_function	ATP hydrolysis 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
B	0000166	molecular_function	nucleotide binding
B	0003677	molecular_function	DNA binding
B	0003678	molecular_function	DNA helicase activity
B	0003697	molecular_function	single-stranded DNA binding
B	0003824	molecular_function	catalytic activity
B	0003899	molecular_function	DNA-directed RNA polymerase 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	0008270	molecular_function	zinc ion binding
B	0016740	molecular_function	transferase activity
B	0016779	molecular_function	nucleotidyltransferase activity
B	0016787	molecular_function	hydrolase activity
B	0016853	molecular_function	isomerase activity
B	0016887	molecular_function	ATP hydrolysis 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
C	0000166	molecular_function	nucleotide binding
C	0003677	molecular_function	DNA binding
C	0003678	molecular_function	DNA helicase activity
C	0003697	molecular_function	single-stranded DNA binding
C	0003824	molecular_function	catalytic activity
C	0003899	molecular_function	DNA-directed RNA polymerase 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	0008270	molecular_function	zinc ion binding
C	0016740	molecular_function	transferase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0016787	molecular_function	hydrolase activity
C	0016853	molecular_function	isomerase activity
C	0016887	molecular_function	ATP hydrolysis 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
D	0000166	molecular_function	nucleotide binding
D	0003677	molecular_function	DNA binding
D	0003678	molecular_function	DNA helicase activity
D	0003697	molecular_function	single-stranded DNA binding
D	0003824	molecular_function	catalytic activity
D	0003899	molecular_function	DNA-directed RNA polymerase 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	0008270	molecular_function	zinc ion binding
D	0016740	molecular_function	transferase activity
D	0016779	molecular_function	nucleotidyltransferase activity
D	0016787	molecular_function	hydrolase activity
D	0016853	molecular_function	isomerase activity
D	0016887	molecular_function	ATP hydrolysis 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
E	0000166	molecular_function	nucleotide binding
E	0003677	molecular_function	DNA binding
E	0003678	molecular_function	DNA helicase activity
E	0003697	molecular_function	single-stranded DNA binding
E	0003824	molecular_function	catalytic activity
E	0003899	molecular_function	DNA-directed RNA polymerase 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	0008270	molecular_function	zinc ion binding
E	0016740	molecular_function	transferase activity
E	0016779	molecular_function	nucleotidyltransferase activity
E	0016787	molecular_function	hydrolase activity
E	0016853	molecular_function	isomerase activity
E	0016887	molecular_function	ATP hydrolysis 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
F	0000166	molecular_function	nucleotide binding
F	0003677	molecular_function	DNA binding
F	0003678	molecular_function	DNA helicase activity
F	0003697	molecular_function	single-stranded DNA binding
F	0003824	molecular_function	catalytic activity
F	0003899	molecular_function	DNA-directed RNA polymerase 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	0008270	molecular_function	zinc ion binding
F	0016740	molecular_function	transferase activity
F	0016779	molecular_function	nucleotidyltransferase activity
F	0016787	molecular_function	hydrolase activity
F	0016853	molecular_function	isomerase activity
F	0016887	molecular_function	ATP hydrolysis 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
H	0000166	molecular_function	nucleotide binding
H	0003676	molecular_function	nucleic acid binding
H	0003677	molecular_function	DNA binding
H	0003824	molecular_function	catalytic activity
H	0003887	molecular_function	DNA-directed DNA polymerase activity
H	0004518	molecular_function	nuclease 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	0016740	molecular_function	transferase activity
H	0016779	molecular_function	nucleotidyltransferase activity
H	0016787	molecular_function	hydrolase 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	17
Details	binding site for residue TTP B 700

Chain	Residue
A	LYS520
B	GLN343
B	HIS465
B	ARG504
B	PRO511
B	ASN512
B	VAL514
B	TYR535
B	MG701
A	ARG522
A	THR524
B	GLY315
B	MET316
B	GLY317
B	LYS318
B	SER319
B	THR320

---

site_id	AC2
Number of Residues	3
Details	binding site for residue MG B 701

Chain	Residue
B	SER319
B	GLN343
B	TTP700

---

site_id	AC3
Number of Residues	14
Details	binding site for residue TTP C 700

Chain	Residue
B	LYS520
B	ARG522
B	GLY525
C	GLY315
C	MET316
C	GLY317
C	LYS318
C	SER319
C	THR320
C	GLN343
C	ARG504
C	ASN512
C	TYR535
C	MG701

---

site_id	AC4
Number of Residues	3
Details	binding site for residue MG C 701

Chain	Residue
C	SER319
C	GLN343
C	TTP700

---

site_id	AC5
Number of Residues	15
Details	binding site for residue TTP D 700

Chain	Residue
C	ARG522
C	PHE523
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	AC6
Number of Residues	3
Details	binding site for residue MG D 701

Chain	Residue
D	SER319
D	GLN343
D	TTP700

---

site_id	AC7
Number of Residues	4
Details	binding site for residue ZN E 601

Chain	Residue
E	CYS17
E	CYS20
E	CYS36
E	CYS39

---

site_id	AC8
Number of Residues	17
Details	binding site for residue TTP E 602

Chain	Residue
D	GLN494
D	ARG522
D	GLY525
E	GLY315
E	MET316
E	GLY317
E	LYS318
E	SER319
E	THR320
E	GLN343
E	HIS465
E	ARG504
E	PRO511
E	ASN512
E	TYR535
E	LYS537
E	MG603

---

site_id	AC9
Number of Residues	3
Details	binding site for residue MG E 603

Chain	Residue
E	SER319
E	GLN343
E	TTP602

---

site_id	AD1
Number of Residues	16
Details	binding site for residue TTP F 700

Chain	Residue
E	CYS521
E	ARG522
E	PHE523
E	GLY525
F	MET316
F	GLY317
F	LYS318
F	SER319
F	THR320
F	GLN343
F	HIS465
F	PRO511
F	ASN512
F	TYR535
F	LYS537
F	MG701

---

site_id	AD2
Number of Residues	3
Details	binding site for residue MG F 701

Chain	Residue
F	SER319
F	GLN343
F	TTP700

---

site_id	AD3
Number of Residues	13
Details	binding site for residue TTP H 801

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

---

site_id	AD4
Number of Residues	4
Details	binding site for residue MG H 802

Chain	Residue
H	ASP475
H	ALA476
H	ASP654
H	TTP801

---

site_id	AD5
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	42
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04154","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI2
Number of Residues	6
Details	Site: {"description":"dTTP/dATP binding","evidences":[{"source":"HAMAP-Rule","id":"MF_04154","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10892646","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI3
Number of Residues	6
Details	Site: {"description":"dTTP/dATP binding","evidences":[{"source":"HAMAP-Rule","id":"MF_04154","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10535735","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI4
Number of Residues	18
Details	Site: {"description":"dTTP/dATP binding","evidences":[{"source":"HAMAP-Rule","id":"MF_04154","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10535735","evidenceCode":"ECO:0000305"},{"source":"PubMed","id":"10892646","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI5
Number of Residues	22
Details	Zinc finger: {"description":"C4-like; zinc ribbon fold","evidences":[{"source":"HAMAP-Rule","id":"MF_04154","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"10200256","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"12769857","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"2829184","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI6
Number of Residues	6
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04154","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"12769857","evidenceCode":"ECO:0000269"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI7
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04154","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"12769857","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI8
Number of Residues	87
Details	Domain: {"description":"Toprim","evidences":[{"source":"PROSITE-ProRule","id":"PRU00995","evidenceCode":"ECO:0000255"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI9
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04101","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"9440688","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI10
Number of Residues	3
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04101","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"9440688","evidenceCode":"ECO:0000269"},{"source":"PubMed","id":"9914251","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---

site_id	SWS_FT_FI11
Number of Residues	4
Details	Binding site: {"evidences":[{"source":"HAMAP-Rule","id":"MF_04101","evidenceCode":"ECO:0000255"},{"source":"PubMed","id":"9914251","evidenceCode":"ECO:0000305"}]}

Chain

Residue

Details

---