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5kfr

Human DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 20 mM Mn2+ for 600s

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

DNA polymerase eta

Homo sapiens

UniProt Q9Y253

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 ;DNA (5'-D(*CP*AP*TP*TP*AP*TP*GP*AP*CP*GP*CP*T)-3') ; × 1 ;DNA (5'-D(*AP*GP*CP*GP*TP*CP*AP*TP*(AS))-3') ; × 1 MANGANESE (II) ION × 2 GLYCEROL × 3 ;2'-DEOXYADENOSINE 5'-O-(1-THIOTRIPHOSPHATE) ; × 1 DIPHOSPHATE × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
2i5o 3wup

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers
3wup

1 assemblies

Heteromeric or nucleic-acid complex
2lsk 3jaa 3mr2 3mr3 3mr5 3mr6 3si8 3tq1 4dl2 4dl3 4dl4 4dl5

239 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name POLH_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–435； UniProt 1–432

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_id5kfr
Deposition date deposition_date2016-06-12
Structure title titleHuman DNA polymerase eta-DNA ternary complex with Sp-dATP-alpha-S: reaction with 20 mM Mn2+ for 600s
Keywords keywordsin crystallo reaction, DNA polymerase, metal ion dependent catalysis, replication, transferase-dna complex; replication, 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.

5kfr__assembly_1__model_1

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

Download this curve (.dat)

5kfr__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.

5kfr__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）24.43 Å
Rg (electron density)24.04 Å
Total Rg24.64 Å
Atom count3802
Residues450
Excluded volume66418 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5kfr__assembly_1__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 (8)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5kfrA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology70 — Alpha-Beta Plaits
Homologous superfamily homologous superfamily270 — Reverse transcriptase/Diguanylate cyclase domain
Domain ID domain_id5kfrA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology1170 — MutS, DNA mismatch repair protein, domain I
Homologous superfamily homologous superfamily60 —
Domain ID domain_id5kfrA03
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_id5kfrA04
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology1490 — Dna Ligase; domain 1
Homologous superfamily homologous superfamily100 — DNA polymerase, Y-family, little finger domain
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7. Citations (1)