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5xma

Crystal structure of AsfvPolX in complex with DNA enzyme at P43212 space group

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

Repair DNA polymerase X

African swine fever virus (strain Badajoz 1971 Vero-adapted)

UniProt P42494

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 2 DNA 2 DNA (36-MER) × 1 ;DNA/RNA (5'-D(*AP*CP*GP*AP*GP*AP*GP*AP*GP*AP*T)-R(P*G)-D(P*GP*GP*TP*GP*CP*GP*TP*TP*AP*CP*A)-3') ; × 1 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1jaj 1jqr 2m2t 2m2u 2m2v

5 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2m2w 5xm8 5xm8 5xm9 5xm9 5xma 8e9a 8e9a 8ild 8ile 8ilf 8ilg

17 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DPOLX_ASFB7
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 4–177； UniProt 1–174 Author chain B； PDBConstruct 4–177； UniProt 1–174

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_id5xma
Deposition date deposition_date2017-05-13
Structure title titleCrystal structure of AsfvPolX in complex with DNA enzyme at P43212 space group
Keywords keywordsPolX, DNA enzyme, 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.

5xma__assembly_1__model_1

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

Download this curve (.dat)

5xma__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.

5xma__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）30.24 Å
Rg (electron density)30.70 Å
Total Rg31.27 Å
Atom count4026
Residues407
Excluded volume69323 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 5xma__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 (3)

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6. Fold Classification (SCOP + CATH) 4 domains

CATH v4.4 (4 domains)

Domain ID domain_id5xmaA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily10 — Beta Polymerase, domain 2
Domain ID domain_id5xmaA02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily10 — DNA polymerase, thumb domain
Domain ID domain_id5xmaB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology460 — Beta Polymerase; domain 2
Homologous superfamily homologous superfamily10 — Beta Polymerase, domain 2
Domain ID domain_id5xmaB02
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology210 — Beta Polymerase; domain 3
Homologous superfamily homologous superfamily10 — DNA polymerase, thumb domain
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7. Citations (1)