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4k8x

Binary complex of 9N DNA polymerase in the replicative state

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

DNA polymerase

Thermococcus

UniProt Q56366

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(P*AP*AP*AP*GP*GP*CP*GP*CP*AP*GP*TP*TP*CP*GP*CP*G)-3') ; × 1 ;DNA (5'-D(*CP*GP*CP*GP*AP*AP*CP*TP*GP*CP*GP*(DOC))-3') ; × 1 SULFATE ION × 11 CHLORIDE ION × 1 ;1-(3-hydroxypropyl)-2-{(1E,3E,5E)-5-[1-(3-hydroxypropyl)-3,3-dimethyl-1,3-dihydro-2H-indol-2-ylidene]penta-1,3-dien-1-y l}-3,3-dimethyl-3H-indolium ; × 1 1,2-ETHANEDIOL × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1qht

1 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
4k8x 5omq 5omv 6is7 6is7 6isf 6isf 6isg 6ish 6isi

10 assemblies

View Construct and Data Evidence
UniProt name DPOL_THES9
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–775； UniProt 1–775

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_id4k8x
Deposition date deposition_date2013-04-19
Structure title titleBinary complex of 9N DNA polymerase in the replicative state
Keywords keywordsDNA polymerase, Binary complex, 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.

4k8x__assembly_1__model_1

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

Download this curve (.dat)

4k8x__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.

4k8x__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）30.16 Å
Rg (electron density)29.60 Å
Total Rg30.29 Å
Atom count6885
Residues786
Excluded volume121270 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4k8x__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_id4k8xA01
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_id4k8xA02
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_id4k8xA03
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_id4k8xA04
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily690 — B family DNA polymerase, finger domain
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7. Citations (1)