Summary Structural details Experimental details Functional details Sequence Neighbor History Downloads

6P7E

Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics the C-terminal Tail of the Primase-Helicase

Functional Information from GO Data

Chain	GOid	namespace	contents
A	0000166	molecular_function	nucleotide binding
A	0003676	molecular_function	nucleic acid binding
A	0003677	molecular_function	DNA binding
A	0003824	molecular_function	catalytic activity
A	0003887	molecular_function	DNA-directed DNA polymerase activity
A	0004518	molecular_function	nuclease activity
A	0004527	molecular_function	exonuclease activity
A	0004529	molecular_function	DNA exonuclease activity
A	0005515	molecular_function	protein binding
A	0006259	biological_process	DNA metabolic process
A	0006260	biological_process	DNA replication
A	0006261	biological_process	DNA-templated DNA replication
A	0006302	biological_process	double-strand break repair
A	0008408	molecular_function	3'-5' exonuclease activity
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
A	0090592	biological_process	DNA synthesis involved in DNA replication
B	0000166	molecular_function	nucleotide binding
B	0003676	molecular_function	nucleic acid binding
B	0003677	molecular_function	DNA binding
B	0003824	molecular_function	catalytic activity
B	0003887	molecular_function	DNA-directed DNA polymerase activity
B	0004518	molecular_function	nuclease activity
B	0004527	molecular_function	exonuclease activity
B	0004529	molecular_function	DNA exonuclease activity
B	0005515	molecular_function	protein binding
B	0006259	biological_process	DNA metabolic process
B	0006260	biological_process	DNA replication
B	0006261	biological_process	DNA-templated DNA replication
B	0006302	biological_process	double-strand break repair
B	0008408	molecular_function	3'-5' exonuclease activity
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
B	0090592	biological_process	DNA synthesis involved in DNA replication
C	0000166	molecular_function	nucleotide binding
C	0003676	molecular_function	nucleic acid binding
C	0003677	molecular_function	DNA binding
C	0003824	molecular_function	catalytic activity
C	0003887	molecular_function	DNA-directed DNA polymerase activity
C	0004518	molecular_function	nuclease activity
C	0004527	molecular_function	exonuclease activity
C	0004529	molecular_function	DNA exonuclease activity
C	0005515	molecular_function	protein binding
C	0006259	biological_process	DNA metabolic process
C	0006260	biological_process	DNA replication
C	0006261	biological_process	DNA-templated DNA replication
C	0006302	biological_process	double-strand break repair
C	0008408	molecular_function	3'-5' exonuclease activity
C	0016740	molecular_function	transferase activity
C	0016779	molecular_function	nucleotidyltransferase activity
C	0016787	molecular_function	hydrolase activity
C	0034061	molecular_function	DNA polymerase activity
C	0039693	biological_process	viral DNA genome replication
C	0046872	molecular_function	metal ion binding
C	0090592	biological_process	DNA synthesis involved in DNA replication
D	0000166	molecular_function	nucleotide binding
D	0003676	molecular_function	nucleic acid binding
D	0003677	molecular_function	DNA binding
D	0003824	molecular_function	catalytic activity
D	0003887	molecular_function	DNA-directed DNA polymerase activity
D	0004518	molecular_function	nuclease activity
D	0004527	molecular_function	exonuclease activity
D	0004529	molecular_function	DNA exonuclease activity
D	0005515	molecular_function	protein binding
D	0006259	biological_process	DNA metabolic process
D	0006260	biological_process	DNA replication
D	0006261	biological_process	DNA-templated DNA replication
D	0006302	biological_process	double-strand break repair
D	0008408	molecular_function	3'-5' exonuclease activity
D	0016740	molecular_function	transferase activity
D	0016779	molecular_function	nucleotidyltransferase activity
D	0016787	molecular_function	hydrolase activity
D	0034061	molecular_function	DNA polymerase activity
D	0039693	biological_process	viral DNA genome replication
D	0046872	molecular_function	metal ion binding
D	0090592	biological_process	DNA synthesis involved in DNA replication
E	0005515	molecular_function	protein binding
E	0005737	cellular_component	cytoplasm
E	0005829	cellular_component	cytosol
E	0015035	molecular_function	protein-disulfide reductase activity
E	0030337	molecular_function	DNA polymerase processivity factor activity
E	0045454	biological_process	cell redox homeostasis
F	0005515	molecular_function	protein binding
F	0005737	cellular_component	cytoplasm
F	0005829	cellular_component	cytosol
F	0015035	molecular_function	protein-disulfide reductase activity
F	0030337	molecular_function	DNA polymerase processivity factor activity
F	0045454	biological_process	cell redox homeostasis
G	0005515	molecular_function	protein binding
G	0005737	cellular_component	cytoplasm
G	0005829	cellular_component	cytosol
G	0015035	molecular_function	protein-disulfide reductase activity
G	0030337	molecular_function	DNA polymerase processivity factor activity
G	0045454	biological_process	cell redox homeostasis
H	0005515	molecular_function	protein binding
H	0005737	cellular_component	cytoplasm
H	0005829	cellular_component	cytosol
H	0015035	molecular_function	protein-disulfide reductase activity
H	0030337	molecular_function	DNA polymerase processivity factor activity
H	0045454	biological_process	cell redox homeostasis

Functional Information from PDB Data

site_id	AC1
Number of Residues	7
Details	binding site for residue TTP A 801

Chain	Residue
A	ALA7
A	ALA8
A	ALA10
A	LEU11
A	TYR64
A	TRP160
A	ASP174

site_id	AC2
Number of Residues	4
Details	binding site for residue MG A 802

Chain	Residue
A	ASP654
A	TTP805
A	ASP475
A	ALA476

site_id	AC3
Number of Residues	6
Details	binding site for residue MG A 803

Chain	Residue
A	ASP475
A	VAL652
A	ASP654
A	GLU655
A	TTP805
I	DA822

site_id	AC4
Number of Residues	5
Details	binding site for residue MG A 804

Chain	Residue
A	HIS59
A	ASP65
A	HOH909
A	HOH914
A	HOH915

site_id	AC5
Number of Residues	15
Details	binding site for residue TTP A 805

Chain	Residue
A	ARG429
A	ASP475
A	ALA476
A	GLY478
A	LEU479
A	GLU480
A	HIS506
A	ARG518
A	LYS522
A	TYR526
A	ASP654
A	MG802
A	MG803
I	DA822
J	DA854

site_id	AC6
Number of Residues	7
Details	binding site for residue TTP B 801

Chain	Residue
B	ALA7
B	ALA8
B	ASN9
B	ALA10
B	TYR64
B	TRP160
B	ASP174

site_id	AC7
Number of Residues	5
Details	binding site for residue MG B 802

Chain	Residue
B	ASP475
B	ALA476
B	ASP654
B	MG803
B	TTP805

site_id	AC8
Number of Residues	6
Details	binding site for residue MG B 803

Chain	Residue
B	ASP475
B	ASP654
B	GLU655
B	MG802
B	TTP805
B	HOH904

site_id	AC9
Number of Residues	3
Details	binding site for residue MG B 804

Chain	Residue
B	HIS59
B	ASP65
B	HOH907

site_id	AD1
Number of Residues	16
Details	binding site for residue TTP B 805

Chain	Residue
B	ARG429
B	ASP475
B	ALA476
B	SER477
B	GLY478
B	LEU479
B	GLU480
B	HIS506
B	ARG518
B	LYS522
B	TYR526
B	ASP654
B	MG802
B	MG803
K	DA822
L	DA854

site_id	AD2
Number of Residues	7
Details	binding site for residue TTP C 801

Chain	Residue
C	ALA7
C	ALA8
C	ALA10
C	LEU11
C	TYR64
C	TRP160
C	ASP174

site_id	AD3
Number of Residues	4
Details	binding site for residue MG C 802

Chain	Residue
C	ASP475
C	ALA476
C	ASP654
C	TTP805

site_id	AD4
Number of Residues	3
Details	binding site for residue MG C 803

Chain	Residue
C	ASP475
C	ASP654
C	TTP805

site_id	AD5
Number of Residues	2
Details	binding site for residue MG C 804

Chain	Residue
C	HIS59
C	ASP65

site_id	AD6
Number of Residues	16
Details	binding site for residue TTP C 805

Chain	Residue
C	THR523
C	TYR526
C	ASP654
C	MG802
C	MG803
M	DA822
N	DA854
C	ARG429
C	ASP475
C	ALA476
C	GLY478
C	LEU479
C	GLU480
C	HIS506
C	ARG518
C	LYS522

site_id	AD7
Number of Residues	8
Details	binding site for residue TTP D 801

Chain	Residue
D	ALA7
D	ALA8
D	ASN9
D	ALA10
D	LEU11
D	TYR64
D	TRP160
D	ASP174

site_id	AD8
Number of Residues	5
Details	binding site for residue MG D 802

Chain	Residue
D	ASP475
D	ALA476
D	ASP654
D	MG803
D	TTP805

site_id	AD9
Number of Residues	4
Details	binding site for residue MG D 803

Chain	Residue
D	ASP475
D	ASP654
D	MG802
D	TTP805

site_id	AE1
Number of Residues	5
Details	binding site for residue MG D 804

Chain	Residue
D	HIS59
D	ASP65
D	HOH901
D	HOH902
D	HOH903

site_id	AE2
Number of Residues	15
Details	binding site for residue TTP D 805

Chain	Residue
D	ARG429
D	ASP475
D	ALA476
D	GLY478
D	LEU479
D	GLU480
D	HIS506
D	ARG518
D	LYS522
D	TYR526
D	ASP654
D	MG802
D	MG803
O	DA822
P	DA854

Functional Information from PROSITE/UniProt

site_id	PS00194
Number of Residues	19
Details	THIOREDOXIN_1 Thioredoxin family active site. LVdFWaeWCGPCKmIapiL

Chain	Residue	Details
E	LEU24-LEU42

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

Chain	Residue	Details
A	ARG518-ILE537

Functional Information from SwissProt/UniProt

site_id	SWS_FT_FI1
Number of Residues	8
Details	ACT_SITE: Nucleophile

Chain	Residue	Details
E	CYS32
D	ALA5
D	ALA7
D	ASP174
E	CYS35
F	CYS32
F	CYS35
G	CYS32
G	CYS35
H	CYS32
H	CYS35
C	ASP174

site_id	SWS_FT_FI2
Number of Residues	4
Details	SITE: Deprotonates C-terminal active site Cys

Chain	Residue	Details
E	ASP26
D	ASP475
D	ALA476
D	ASP654
F	ASP26
G	ASP26
H	ASP26
B	ALA476
B	ASP654
C	ASP475
C	ALA476
C	ASP654

site_id	SWS_FT_FI3
Number of Residues	8
Details	SITE: Contributes to redox potential value

Chain	Residue	Details
E	GLY33
C	ARG518
C	LYS522
C	TYR526
D	HIS506
D	ARG518
D	LYS522
D	TYR526
E	PRO34
F	GLY33
F	PRO34
G	GLY33
G	PRO34
H	GLY33
H	PRO34
C	HIS506

site_id	SWS_FT_FI4
Number of Residues	4
Details	MOD_RES: N6-acetyllysine => ECO:0000269\|PubMed:18723842

Chain	Residue	Details
E	LYS69
F	LYS69
G	LYS69
H	LYS69

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