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2dy4

Crystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol

Method: X-RAY DIFFRACTION
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1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA polymerase

Enterobacteria phage RB69

UniProt Q38087

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3' × 1 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3' × 1 water × 3 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3' × 1 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3' × 1 water × 3 Consistent with all polymers
3 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3' × 1 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3' × 1 water × 3 Consistent with all polymers
4 Protein–DNA Monomer Protein 1 DNA 2 5'-D(*CP*GP*(CTG)P*GP*GP*AP*AP*TP*GP*A*CP*AP*GP*CP*CP*GP*CP*G)-3' × 1 5'-D(*GP*CP*GP*GP*CP*TP*GP*T*CP*AP*TP*TP*CP*CP*A)-3' × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1ih7 1waf 1waf 1waj 3cfo 4i9l

6 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1b8h 1clq 1ig9 1q9x 1q9x 1q9x 1q9x 1q9y 2atq 2dtu 2dtu 2dtu

161 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DPOL_BPR69
Isoform —
PDB entities 3
Chains and sequence ranges Author chain A； PDBConstruct 1–903； UniProt 1–903 Author chain B； PDBConstruct 1–903； UniProt 1–903 Author chain C； PDBConstruct 1–903； UniProt 1–903 Author chain D； PDBConstruct 1–903； UniProt 1–903

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_id2dy4
Deposition date deposition_date2006-09-06
Structure title titleCrystal structure of RB69 GP43 in complex with DNA containing Thymine Glycol
Keywords keywordsDNA polymerase, DNA lesion, thymine glycol, oxidative thymine lesion, TRANSFERASE-DNA COMPLEX; TRANSFERASE/DNA
Experimental Method methodX-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.

2dy4__assembly_1__model_1

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

Download this curve (.dat)

2dy4__assembly_1__model_1 | I(q)

10-2 10-1 106 107 108 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

2dy4__assembly_1__model_1 | P(r) · Pending

The new assembly/model P(r) has not been calculated yet This placeholder does not display legacy data r (Angstrom) P(r)
P(r) will be calculated and displayed separately for the same assembly/model.
Rg（Guinier）33.10 Å
Rg (electron density)32.05 Å
Total Rg32.67 Å
Atom count7926
Residues907
Excluded volume139650 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 2dy4__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 2dy4__assembly_2__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
3 1 2dy4__assembly_3__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
4 1 2dy4__assembly_4__model_1 trimeric （3） 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 (4)

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6. Fold Classification (SCOP + CATH) 32 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd2dy4a1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.5 — DnaQ-like 3'-5' exonuclease
Domain ID domain_idd2dy4a2
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.1 — DNA polymerase I
Domain ID domain_idd2dy4b1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.5 — DnaQ-like 3'-5' exonuclease
Domain ID domain_idd2dy4b2
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.1 — DNA polymerase I
Domain ID domain_idd2dy4c1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.5 — DnaQ-like 3'-5' exonuclease
Domain ID domain_idd2dy4c2
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.1 — DNA polymerase I
Domain ID domain_idd2dy4d1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamilyc.55.3 — Ribonuclease H-like
Family Family familyc.55.3.5 — DnaQ-like 3'-5' exonuclease
Domain ID domain_idd2dy4d2
Class classe — Multi-domain proteins (alpha and beta)
Fold Fold folde.8 — DNA/RNA polymerases
Superfamily Superfamily superfamilye.8.1 — DNA/RNA polymerases
Family Family familye.8.1.1 — DNA polymerase I

CATH v4.4 (24 domains)

Domain ID domain_id2dy4A01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology342 — DNA Polymerase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — DNA Polymerase, chain B, domain 1
Domain ID domain_id2dy4A02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2dy4A03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily10 — B family DNA polymerase, palm domain
Domain ID domain_id2dy4A04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily690 — B family DNA polymerase, finger domain
Domain ID domain_id2dy4A05
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily300 —
Domain ID domain_id2dy4A06
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1820 — Ribonuclease H-like motif
Homologous superfamily homologous superfamily10 — DnaQ-like 3'-5' exonuclease
Domain ID domain_id2dy4B01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology342 — DNA Polymerase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — DNA Polymerase, chain B, domain 1
Domain ID domain_id2dy4B02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2dy4B03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily10 — B family DNA polymerase, palm domain
Domain ID domain_id2dy4B04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily690 — B family DNA polymerase, finger domain
Domain ID domain_id2dy4B05
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily300 —
Domain ID domain_id2dy4B06
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1820 — Ribonuclease H-like motif
Homologous superfamily homologous superfamily10 — DnaQ-like 3'-5' exonuclease
Domain ID domain_id2dy4C01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology342 — DNA Polymerase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — DNA Polymerase, chain B, domain 1
Domain ID domain_id2dy4C02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2dy4C03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily10 — B family DNA polymerase, palm domain
Domain ID domain_id2dy4C04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily690 — B family DNA polymerase, finger domain
Domain ID domain_id2dy4C05
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily300 —
Domain ID domain_id2dy4C06
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1820 — Ribonuclease H-like motif
Homologous superfamily homologous superfamily10 — DnaQ-like 3'-5' exonuclease
Domain ID domain_id2dy4D01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology342 — DNA Polymerase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — DNA Polymerase, chain B, domain 1
Domain ID domain_id2dy4D02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily10 — Ribonuclease H-like superfamily/Ribonuclease H
Domain ID domain_id2dy4D03
Class class3 — Alpha Beta
Architecture architecture90 — Alpha-Beta Complex
Topology topology1600 — Palm domain of DNA polymerase
Homologous superfamily homologous superfamily10 — B family DNA polymerase, palm domain
Domain ID domain_id2dy4D04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily690 — B family DNA polymerase, finger domain
Domain ID domain_id2dy4D05
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1280 — Monooxygenase
Homologous superfamily homologous superfamily300 —
Domain ID domain_id2dy4D06
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1820 — Ribonuclease H-like motif
Homologous superfamily homologous superfamily10 — DnaQ-like 3'-5' exonuclease
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7. Citations (1)