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6nku

Ternary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with dGTP

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

DNA polymerase beta

Homo sapiens

UniProt P06746

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Monomer Protein 1 DNA 3 ;DNA (5'-D(*CP*CP*GP*AP*AP*CP*AP*AP*GP*CP*AP*TP*CP*AP*GP*C)-3') ; × 1 ;DNA (5'-D(*GP*CP*TP*GP*AP*TP*GP*CP*TP*(2DT))-3') ; × 1 ;DNA (5'-D(P*TP*TP*CP*GP*G)-3') ; × 1 MAGNESIUM ION × 2 SODIUM ION × 3 CHLORIDE ION × 4 2'-DEOXYGUANOSINE-5'-TRIPHOSPHATE × 1 water × 4 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer

None

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1bpx 1bpy 1bpz 1mq2 1mq3 1tv9 1tva 1zjm 1zjn 1zqa 1zqb 1zqc

434 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DPOLB_HUMAN
Isoform —
PDB entities 4
Chains and sequence ranges Author chain A； PDBConstruct 1–335； UniProt 1–335

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_id6nku
Deposition date deposition_date2019-01-07
Structure title titleTernary complex crystal structure of DNA polymerase Beta with "hot-spot sequence" with dGTP
Keywords keywordsDNA Polymerase Beta, Conformational Change, enzyme mechanism, transcription-dna complex; transcription/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.

6nku__assembly_1__model_1

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

Download this curve (.dat)

6nku__assembly_1__model_1 | I(q)

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

6nku__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）22.92 Å
Rg (electron density)22.21 Å
Total Rg22.97 Å
Atom count3280
Residues356
Excluded volume56396 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 6nku__assembly_1__model_1 tetrameric （4） 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 (9)

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6. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id6nkuA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily110 — DNA polymerase beta, N-terminal domain-like
Domain ID domain_id6nkuA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily20 — 5' to 3' exonuclease, C-terminal subdomain
Domain ID domain_id6nkuA03
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily10 — Beta Polymerase, domain 2
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7. Citations (1)