2ex3

Bacteriophage phi29 DNA polymerase bound to terminal protein

Method: X-RAY DIFFRACTION

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

DNA polymerase

Bacillus phage phi29

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA terminal protein × 1 （P03681） LEAD (II) ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA terminal protein × 1 （P03681） LEAD (II) ION × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	DNA terminal protein × 1 （P03681） LEAD (II) ION × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	DNA terminal protein × 1 （P03681） LEAD (II) ION × 3	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	DNA terminal protein × 1 （P03681） LEAD (II) ION × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	DNA terminal protein × 1 （P03681） LEAD (II) ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DPOL_BPPH2
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–575； UniProt 1–575 Author chain C； PDBConstruct 1–575； UniProt 1–575 Author chain E； PDBConstruct 1–575； UniProt 1–575 Author chain G； PDBConstruct 1–575； UniProt 1–575 Author chain I； PDBConstruct 1–575； UniProt 1–575 Author chain K； PDBConstruct 1–575； UniProt 1–575

DNA terminal protein

Bacillus phage phi29

UniProt P03681

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase × 1 （P03680） LEAD (II) ION × 3	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase × 1 （P03680） LEAD (II) ION × 3	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase × 1 （P03680） LEAD (II) ION × 3	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase × 1 （P03680） LEAD (II) ION × 3	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase × 1 （P03680） LEAD (II) ION × 2	Consistent with protein count
6	Protein heterocomplex	Heteromer	Protein 2	DNA polymerase × 1 （P03680） LEAD (II) ION × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	TERM_BPPH2
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 35–230； UniProt 71–266 Author chain D； PDBConstruct 35–230； UniProt 71–266 Author chain F； PDBConstruct 35–230； UniProt 71–266 Author chain H； PDBConstruct 35–230； UniProt 71–266 Author chain J； PDBConstruct 35–230； UniProt 71–266 Author chain L； PDBConstruct 35–230； UniProt 71–266

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	2ex3
Deposition date deposition_date	2005-11-07
Structure title title	Bacteriophage phi29 DNA polymerase bound to terminal protein
Keywords keywords	DNA POLYMERASE: PROTEIN PRIMER COMPLEX, transferase-replication COMPLEX; transferase/replication
Experimental Method method	X-RAY DIFFRACTION

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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.

2ex3__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

2ex3__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2ex3__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	31.20 Å
Rg (electron density)	30.36 Å
Total Rg	30.91 Å
Atom count	6185
Residues	766
Excluded volume	110970 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2ex3__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2ex3__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`2ex3__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`2ex3__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`2ex3__assembly_5__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`2ex3__assembly_6__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download

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4. Crystallography and Experiment 4. Crystallography & Experiment

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5. Entities and Polymers Entities & Polymers (3)

Entity 1 Entity 1 polymer

Description description	DNA polymerase
Molecular weight formula_weight	66720.9 kDa
EC 编号 ec_number	2.7.7.7
Mutation mutation	D12A/D66A
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C,E,G,I,K
Atom count atom_count	37108

MKHMPRKMYSCAFETTTKVEDCRVWAYGYMNIEDHSEYKIGNSLDEFMAWVLKVQADLYFHNLKFAGAFIINWLERNGFKWSADGLPNTYNTIISRMGQWYMIDICLGYKGKRKIHTVIYDSLKKLPFPVKKIAKDFKLTVLKGDIDYHKERPVGYKITPEEYAYIKNDIQIIAEALLIQFKQGLDRMTAGSDSLKGFKDIITTKKFKKVFPTLSLGLDKEVRYAYRGGFTWLNDRFKEKEIGEGMVFDVNSLYPAQMYSRLLPYGEPIVFEGKYVWDEDYPLHIQHIRCEFELKEGYIPTIQIKRSRFYKGNEYLKSSGGEIADLWLSNVDLELMKEHYDLYNVEYISGLKFKATTGLFKDFIDKWTYIKTTSEGAIKQLAKLMLNSLYGKFASNPDVTGKVPYLKENGALGFRLGEEETKDPVYTPMGVFITAWARYTTITAAQACYDRIIYCDTDSIHLTGTEIPDVIKDIVDPKKLGYWAHESTFKRAKYLRQKTYIQDIYMKEVDGKLVEGSPDDYTDIKFSVKCAGMTDKIKKEVTFENFKVGFSRKMKPKPVQVPGGVVLVDDTFTIK

Source Source

Source organism organism	Bacillus phage phi29
NCBI taxonomy ID ncbi_taxonomy_id	10756
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	DNA terminal protein
Molecular weight formula_weight	25816.4 kDa
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D,F,H,J,L

XXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXANMRYQFEKNAYGVVASKAKIAEIERNTKEVQRLVDEKIKAMKDKEYYAGGKPQGTIEQRIAMTSPAHVTGINRPHDFDFSKVRSYSRLRTLEESMEMRTDPQYYEKKMIQLQLNFIKSVEGSFNSFDAADELIEELKKIPPDDFYELFLRISEISFEEFDSEGNTVENVEGNVYKILSYLEQYRRGDFDLSLKGF

Source Source

Source organism organism	Bacillus phage phi29
NCBI taxonomy ID ncbi_taxonomy_id	10756
Host organism host_organism	Bacillus subtilis

Entity 3 Entity 3 non-polymer

Description description	LEAD (II) ION
Molecular weight formula_weight	207.2 kDa
Source method src_method	syn
Copy count entity_count	16

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6. Fold Classification (SCOP + CATH) 66 domains

SCOP 2.08 (18 domains)

Domain ID domain_id	d2ex3a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

Domain ID domain_id	d2ex3a2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.1 — DNA polymerase I

Domain ID domain_id	d2ex3b1
Class class	a — All alpha proteins
Fold Fold fold	a.263 — DNA terminal protein
Superfamily Superfamily superfamily	a.263.1 — DNA terminal protein
Family Family family	a.263.1.1 — DNA terminal protein

Domain ID domain_id	d2ex3c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

Domain ID domain_id	d2ex3c2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.1 — DNA polymerase I

Domain ID domain_id	d2ex3d1
Class class	a — All alpha proteins
Fold Fold fold	a.263 — DNA terminal protein
Superfamily Superfamily superfamily	a.263.1 — DNA terminal protein
Family Family family	a.263.1.1 — DNA terminal protein

Domain ID domain_id	d2ex3e1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

Domain ID domain_id	d2ex3e2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.1 — DNA polymerase I

Domain ID domain_id	d2ex3f1
Class class	a — All alpha proteins
Fold Fold fold	a.263 — DNA terminal protein
Superfamily Superfamily superfamily	a.263.1 — DNA terminal protein
Family Family family	a.263.1.1 — DNA terminal protein

Domain ID domain_id	d2ex3g1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

Domain ID domain_id	d2ex3g2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.1 — DNA polymerase I

Domain ID domain_id	d2ex3h1
Class class	a — All alpha proteins
Fold Fold fold	a.263 — DNA terminal protein
Superfamily Superfamily superfamily	a.263.1 — DNA terminal protein
Family Family family	a.263.1.1 — DNA terminal protein

Domain ID domain_id	d2ex3i1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

Domain ID domain_id	d2ex3i2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.1 — DNA polymerase I

Domain ID domain_id	d2ex3j1
Class class	a — All alpha proteins
Fold Fold fold	a.263 — DNA terminal protein
Superfamily Superfamily superfamily	a.263.1 — DNA terminal protein
Family Family family	a.263.1.1 — DNA terminal protein

Domain ID domain_id	d2ex3k1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.3 — Ribonuclease H-like
Family Family family	c.55.3.5 — DnaQ-like 3'-5' exonuclease

Domain ID domain_id	d2ex3k2
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.8 — DNA/RNA polymerases
Superfamily Superfamily superfamily	e.8.1 — DNA/RNA polymerases
Family Family family	e.8.1.1 — DNA polymerase I

Domain ID domain_id	d2ex3l1
Class class	a — All alpha proteins
Fold Fold fold	a.263 — DNA terminal protein
Superfamily Superfamily superfamily	a.263.1 — DNA terminal protein
Family Family family	a.263.1.1 — DNA terminal protein

CATH v4.4 (48 domains)

Domain ID domain_id	2ex3A01
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	2ex3A02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — B family DNA polymerase, palm domain

Domain ID domain_id	2ex3A03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1770 — TPR 1 domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — TPR 1 domain of DNA polymerase

Domain ID domain_id	2ex3A04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	690 — B family DNA polymerase, finger domain

Domain ID domain_id	2ex3A05
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	20 — DNA polymerase; domain 5

Domain ID domain_id	2ex3A06
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	30 — DNA polymerase; domain 6

Domain ID domain_id	2ex3B01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	960 —

Domain ID domain_id	2ex3B02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	230 — DNA terminal protein Gp3, priming domain

Domain ID domain_id	2ex3C01
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	2ex3C02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — B family DNA polymerase, palm domain

Domain ID domain_id	2ex3C03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1770 — TPR 1 domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — TPR 1 domain of DNA polymerase

Domain ID domain_id	2ex3C04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	690 — B family DNA polymerase, finger domain

Domain ID domain_id	2ex3C05
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	20 — DNA polymerase; domain 5

Domain ID domain_id	2ex3C06
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	30 — DNA polymerase; domain 6

Domain ID domain_id	2ex3D01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	960 —

Domain ID domain_id	2ex3D02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	230 — DNA terminal protein Gp3, priming domain

Domain ID domain_id	2ex3E01
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	2ex3E02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — B family DNA polymerase, palm domain

Domain ID domain_id	2ex3E03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1770 — TPR 1 domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — TPR 1 domain of DNA polymerase

Domain ID domain_id	2ex3E04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	690 — B family DNA polymerase, finger domain

Domain ID domain_id	2ex3E05
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	20 — DNA polymerase; domain 5

Domain ID domain_id	2ex3E06
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	30 — DNA polymerase; domain 6

Domain ID domain_id	2ex3F01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	960 —

Domain ID domain_id	2ex3F02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	230 — DNA terminal protein Gp3, priming domain

Domain ID domain_id	2ex3G01
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	2ex3G02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — B family DNA polymerase, palm domain

Domain ID domain_id	2ex3G03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1770 — TPR 1 domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — TPR 1 domain of DNA polymerase

Domain ID domain_id	2ex3G04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	690 — B family DNA polymerase, finger domain

Domain ID domain_id	2ex3G05
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	20 — DNA polymerase; domain 5

Domain ID domain_id	2ex3G06
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	30 — DNA polymerase; domain 6

Domain ID domain_id	2ex3H01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	960 —

Domain ID domain_id	2ex3H02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	230 — DNA terminal protein Gp3, priming domain

Domain ID domain_id	2ex3I01
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	2ex3I02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — B family DNA polymerase, palm domain

Domain ID domain_id	2ex3I03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1770 — TPR 1 domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — TPR 1 domain of DNA polymerase

Domain ID domain_id	2ex3I04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	690 — B family DNA polymerase, finger domain

Domain ID domain_id	2ex3I05
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	20 — DNA polymerase; domain 5

Domain ID domain_id	2ex3I06
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	30 — DNA polymerase; domain 6

Domain ID domain_id	2ex3J01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	960 —

Domain ID domain_id	2ex3J02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	230 — DNA terminal protein Gp3, priming domain

Domain ID domain_id	2ex3K01
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	2ex3K02
Class class	3 — Alpha Beta
Architecture architecture	90 — Alpha-Beta Complex
Topology topology	1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — B family DNA polymerase, palm domain

Domain ID domain_id	2ex3K03
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1770 — TPR 1 domain of DNA polymerase
Homologous superfamily homologous superfamily	10 — TPR 1 domain of DNA polymerase

Domain ID domain_id	2ex3K04
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	690 — B family DNA polymerase, finger domain

Domain ID domain_id	2ex3K05
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	20 — DNA polymerase; domain 5

Domain ID domain_id	2ex3K06
Class class	4 — Few Secondary Structures
Architecture architecture	10 — Irregular
Topology topology	80 — Rhinovirus 14, subunit 4
Homologous superfamily homologous superfamily	30 — DNA polymerase; domain 6

Domain ID domain_id	2ex3L01
Class class	6 — Special
Architecture architecture	10 — Helix non-globular
Topology topology	250 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	960 —

Domain ID domain_id	2ex3L02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1270 — Substrate Binding Domain Of Dnak; Chain:A; Domain 2
Homologous superfamily homologous superfamily	230 — DNA terminal protein Gp3, priming domain

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Unit-cell length a length_a	304.933 Å
Unit-cell length b length_b	220.281 Å
Unit-cell length c length_c	217.165 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	45.40 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	24

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	48.850 Å
R factor r_factor	0.2030
R_work r_work	0.2000
R_free r_free	0.2290

Bacteriophage phi29 DNA polymerase bound to terminal protein

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

DNA polymerase

State in the Current Structure

Other States of the Same Protein in the Database

DNA terminal protein

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

2ex3__assembly_3__model_1

2ex3__assembly_3__model_1 | I(q)

2ex3__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 66 domains

SCOP 2.08 (18 domains)

CATH v4.4 (48 domains)

7. Citations (1)

Bacteriophage phi29 DNA polymerase bound to terminal protein

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

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

DNA terminal protein

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

2ex3__assembly_3__model_1

2ex3__assembly_3__model_1 | I(q)

2ex3__assembly_3__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 (3)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Source Source

Entity 3 Entity 3 non-polymer

6. Fold Classification (SCOP + CATH) 66 domains

SCOP 2.08 (18 domains)

CATH v4.4 (48 domains)

7. Citations (1)