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4u7c

Structure of DNA polymerase kappa in complex with benzopyrene adducted DNA

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

DNA polymerase kappa

Homo sapiens

UniProt Q9UBT6

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*GP*CP*GP*GP*AP*TP*CP*AP*G)-3') ; × 1 ;DNA (5'-D(*P*AP*TP*GP*(VKJ)P*CP*TP*GP*AP*TP*CP*CP*GP*C)-3') ; × 1 MAGNESIUM ION × 1 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 DI(HYDROXYETHYL)ETHER × 1 water × 3 Consistent with all polymers
2 Protein–DNA Monomer Protein 1 DNA 2 ;DNA (5'-D(P*GP*CP*GP*GP*AP*TP*CP*AP*G)-3') ; × 1 ;DNA (5'-D(*P*AP*TP*GP*(VKJ)P*CP*TP*GP*AP*TP*CP*CP*GP*C)-3') ; × 1 MAGNESIUM ION × 1 2'-deoxy-5'-O-[(R)-hydroxy{[(R)-hydroxy(phosphonooxy)phosphoryl]amino}phosphoryl]cytidine × 1 DI(HYDROXYETHYL)ETHER × 2 1,2-ETHANEDIOL × 1 water × 3 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1t94 1t94

2 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2lsi 2oh2 2oh2 2w7o 2w7o 2w7p 2w7p 3in5 3in5 3pzp 3pzp 4ba9

31 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name POLK_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–492； UniProt 27–518 Author chain B； PDBConstruct 1–492； UniProt 27–518

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_id4u7c
Deposition date deposition_date2014-07-30
Structure title titleStructure of DNA polymerase kappa in complex with benzopyrene adducted DNA
Keywords keywordsbenzo[a]pyrene-N2-Guanine, DNA replication, DNA damage tolerance, polymerase kappa, Environment pollution, 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.

4u7c__assembly_1__model_1

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

Download this curve (.dat)

4u7c__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.

4u7c__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）24.96 Å
Rg (electron density)24.54 Å
Total Rg25.23 Å
Atom count3894
Residues452
Excluded volume68084 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 4u7c__assembly_1__model_1 trimeric （3） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 4u7c__assembly_2__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) 8 domains

CATH v4.4 (8 domains)

Domain ID domain_id4u7cA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily810 —
Domain ID domain_id4u7cA02
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_id4u7cA03
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_id4u7cA04
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
Domain ID domain_id4u7cB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily810 —
Domain ID domain_id4u7cB02
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_id4u7cB03
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_id4u7cB04
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)