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

Method: X-RAY DIFFRACTION

▼

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed DNA polymerase

Enterobacteria phage T7

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 3 DNA 2	TrxA × 1 （Q14F07） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGP*A)-3') ; × 1 DNA (25-MER) × 1 ASP-THR-ASP-PHE peptide × 1 THYMIDINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 3 water × 2	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 3 DNA 2	TrxA × 1 （Q14F07） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGP*A)-3') ; × 1 DNA (25-MER) × 1 ASP-THR-ASP-PHE peptide × 1 THYMIDINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 3 water × 3	Consistent with all polymers
3	Protein–DNA	Heteromer	Protein 3 DNA 2	TrxA × 1 （Q14F07） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGP*A)-3') ; × 1 DNA (25-MER) × 1 THR-ASP-PHE peptide × 1 THYMIDINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 3 water × 1	Consistent with all polymers
4	Protein–DNA	Heteromer	Protein 2 DNA 2	TrxA × 1 （Q14F07） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGP*A)-3') ; × 1 DNA (25-MER) × 1 THYMIDINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 3 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOL_BPT7
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–704； UniProt 1–704 Author chain B； PDBConstruct 1–704； UniProt 1–704 Author chain C； PDBConstruct 1–704； UniProt 1–704 Author chain D； PDBConstruct 1–704； UniProt 1–704

TrxA

Escherichia coli

UniProt Q14F07

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Heteromer	Protein 3 DNA 2	DNA-directed DNA polymerase × 1 （P00581） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGP*A)-3') ; × 1 DNA (25-MER) × 1 ASP-THR-ASP-PHE peptide × 1 THYMIDINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 3 water × 2	Consistent with all polymers
2	Protein–DNA	Heteromer	Protein 3 DNA 2	DNA-directed DNA polymerase × 1 （P00581） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGP*A)-3') ; × 1 DNA (25-MER) × 1 ASP-THR-ASP-PHE peptide × 1 THYMIDINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 3 water × 3	Consistent with all polymers
3	Protein–DNA	Heteromer	Protein 3 DNA 2	DNA-directed DNA polymerase × 1 （P00581） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGP*A)-3') ; × 1 DNA (25-MER) × 1 THR-ASP-PHE peptide × 1 THYMIDINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 3 water × 1	Consistent with all polymers
4	Protein–DNA	Heteromer	Protein 2 DNA 2	DNA-directed DNA polymerase × 1 （P00581） ;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGP*A)-3') ; × 1 DNA (25-MER) × 1 THYMIDINE-5'-TRIPHOSPHATE × 2 MAGNESIUM ION × 3 water × 1	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q14F07_ECOLX
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain E； PDBConstruct 1–109； UniProt 36–144 Author chain F； PDBConstruct 1–109； UniProt 36–144 Author chain G； PDBConstruct 1–109； UniProt 36–144 Author chain H； PDBConstruct 1–109； UniProt 36–144

The page prioritizes protein identity, the current assembly, associated components, oligomeric state and cross-PDB links. Chain mapping and sequence ranges are retained as data evidence. Internal IDs, import timestamps and assembly operation expressions are maintenance fields and are not shown here.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	6p7e
Deposition date deposition_date	2019-06-05
Structure title title	Structure of T7 DNA Polymerase Bound to a Primer/Template DNA and a Peptide that Mimics the C-terminal Tail of the Primase-Helicase
Keywords keywords	DNA Replication, DNA polymerase, DNA binding protein, TRANSFERASE-DNA BINDING PROTEIN-DNA complex; TRANSFERASE/DNA BINDING PROTEIN/DNA
Experimental Method method	X-RAY DIFFRACTION

▼

3. Official assembly/model SAXS Official SAXS Profiles

This page reads only the latest assembly calculations. Every curve maps to an explicit PDB entry, official biological assembly and coordinate model.

6p7e__assembly_1__model_1

Assembly 1 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

6p7e__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6p7e__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	33.18 Å
Rg (electron density)	33.40 Å
Total Rg	33.81 Å
Atom count	7367
Residues	849
Excluded volume	127730 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6p7e__assembly_1__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6p7e__assembly_2__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`6p7e__assembly_3__model_1`	pentameric （5）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`6p7e__assembly_4__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Description description	DNA-directed DNA polymerase
Molecular weight formula_weight	79703.6 kDa
EC 编号 ec_number	2.7.7.7,3.1.11.-
Mutation mutation	D5A, E7A
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	28831

MIVSAIAANALLESVTKFHCGVIYDYSTAEYVSYRPSDFGAYLDALEAEVARGGLIVFHNGHKYDVPALTKLAKLQLNREFHLPRENCIDTLVLSRLIHSNLKDTDMGLLRSGKLPGKRFGSHALEAWGYRLGEMKGEYKDDFKRMLEEQGEEYVDGMEWWNFNEEMMDYNVQDVVVTKALLEKLLSDKHYFPPEIDFTDVGYTTFWSESLEAVDIEHRAAWLLAKQERNGFPFDTKAIEELYVELAARRSELLRKLTETFGSWYQPKGGTEMFCHPRTGKPLPKYPRIKTPKVGGIFKKPKNKAQREGREPCELDTREYVAGAPYTPVEHVVFNPSSRDHIQKKLQEAGWVPTKYTDKGAPVVDDEVLEGVRVDDPEKQAAIDLIKEYLMIQKRIGQSAEGDKAWLRYVAEDGKIHGSVNPNGAVTGRATHAFPNLAQIPGVRSPYGEQCRAAFGAEHHLDGITGKPWVQAGIDASGLELRCLAHFMARFDNGEYAHEILNGDIHTKNQIAAELPTRDNAKTFIYGFLYGAGDEKIGQIVGAGKERGKELKKKFLENTPAIAALRESIQQTLVESSQWVAGEQQVKWKRRWIKGLDGRKVHVRSPHAALNTLLQSAGALICKLWIIKTEEMLVEKGLKHGWDGDFAYMAWVHDEIQVGCRTEEIAQVVIETAQEAMRWVGDHWNFRCLLDTEGKMGPNWAICH

Source Source

Source organism organism	Enterobacteria phage T7
Common name common_name	Bacteriophage T7
NCBI taxonomy ID ncbi_taxonomy_id	10760
Host organism host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 polymer

Description description	TrxA
Molecular weight formula_weight	11818.6 kDa
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	E,F,G,H

MSDKIIHLTDDSFDTDVLKADGAILVDFWAEWCGPCKMIAPILDEIADEYQGKLTVAKLNIDQNPGTAPKYGIRGIPTLLLFKNGEVAATKVGALSKGQLKEFLDANLA

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PGPGPCPAPGPGPTPGPGPTPCPTPTPGPCPCPGPGPTPGP*A)-3') ;
Molecular weight formula_weight	6551.2 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,K,M,O

GGCAGGTGGTCTTGCCGGTGA

Entity 4 Entity 4 polymer

Description description	DNA (25-MER)
Molecular weight formula_weight	7518.9 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	J,L,N,P

CCCATCACCGGCAAGACCACCTGCC

Entity 5 Entity 5 polymer

Description description	ASP-THR-ASP-PHE peptide
Molecular weight formula_weight	496.5 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	U,V

DTDF

Entity 6 Entity 6 polymer

Description description	THR-ASP-PHE peptide
Molecular weight formula_weight	381.4 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	W

TDF

Entity 7 Entity 7 non-polymer

Description description	THYMIDINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	482.2 kDa
Source method src_method	syn
Copy count entity_count	8

Entity 8 Entity 8 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	12

Entity 9 Entity 9 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	31

▼

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

Domain ID domain_id	6p7eA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	6p7eA02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1060 — Taq DNA Polymerase; Chain T, domain 4
Homologous superfamily homologous superfamily	10 — Taq DNA Polymerase; Chain T, domain 4

Domain ID domain_id	6p7eB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	6p7eC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	6p7eD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	10 — Ribonuclease H-like superfamily/Ribonuclease H

Domain ID domain_id	6p7eE01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	6p7eF01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	6p7eG01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

Domain ID domain_id	6p7eH01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	30 — Glutaredoxin
Homologous superfamily homologous superfamily	10 — Glutaredoxin

▶

Unit-cell length a length_a	100.724 Å
Unit-cell length b length_b	102.698 Å
Unit-cell length c length_c	148.885 Å
Unit-cell angle α angle_alpha	91.36 °
Unit-cell angle β angle_beta	96.83 °
Unit-cell angle γ angle_gamma	113.11 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1
Space-group number int_tables_number	1
Crystal system crystal_system	—

Resolution resolution	3.001 Å
Low-resolution limit resolution_low	49.129 Å
R factor r_factor	0.2159
R_work r_work	0.2142
R_free r_free	0.2481

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed DNA polymerase

State in the Current Structure

Other States of the Same Protein in the Database

TrxA

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6p7e__assembly_1__model_1

6p7e__assembly_1__model_1 | I(q)

6p7e__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)

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

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-directed DNA polymerase

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

TrxA

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

6p7e__assembly_1__model_1

6p7e__assembly_1__model_1 | I(q)

6p7e__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (9)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 polymer

Polymer Polymer

Entity 5 Entity 5 polymer

Polymer Polymer

Entity 6 Entity 6 polymer

Polymer Polymer

Entity 7 Entity 7 non-polymer

Entity 8 Entity 8 non-polymer

Entity 9 Entity 9 water

6. Fold Classification (SCOP + CATH) 9 domains

CATH v4.4 (9 domains)

7. Citations (1)