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3k75

X-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic domain

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

DNA repair protein XRCC1

Homo sapiens

UniProt P18887

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 DNA polymerase beta × 1 （P06766） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 DNA polymerase beta × 1 （P06766） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1cdz 1xna 1xnt 2d8m 3k77 3k77 3k77 3k77 3k77 3k77 3k77 3k77

12 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
2w3o 2w3o 3k75 3k75 3lqc 5e6q 5w7x 5w7x 5w7x 5w7x 5w7y 5w7y

12 assemblies

View Construct and Data Evidence
UniProt name XRCC1_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain B； PDBConstruct 1–183； UniProt 1–183 Author chain C； PDBConstruct 1–183； UniProt 1–183

DNA polymerase beta

Rattus norvegicus

UniProt P06766

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein heterocomplex Heteromer Protein 2 DNA repair protein XRCC1 × 1 （P18887） Consistent with protein count
2 Protein heterocomplex Heteromer Protein 2 DNA repair protein XRCC1 × 1 （P18887） Consistent with protein count

Other States of the Same Protein in the Database

Monomer
1bno 1bnp 1bpb 1bpd 1bpe 1dk2 1dk3 1jn3 1nom 1rpl 1zqu 1zqv

23 assemblies; showing the first 12

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1huo 1huo 1huz 1huz 2bpf 2bpg 2bpg 3k75 3k75 3lqc 3uxp 3uxp

15 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name DPOLB_RAT
Isoform —
PDB entities 2
Chains and sequence ranges Author chain D； PDBConstruct 2–246； UniProt 91–335 Author chain E； PDBConstruct 2–246； UniProt 91–335

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_id3k75
Deposition date deposition_date2009-10-12
Structure title titleX-ray crystal structure of reduced XRCC1 bound to DNA pol beta catalytic domain
Keywords keywords;allosteric disulfide, XRCC1, pol beta, DNA damage, DNA repair, Nucleus, Phosphoprotein, DNA replication, DNA synthesis, DNA-binding, DNA-directed DNA polymerase, Lyase, Magnesium, Metal-binding, Methylation, Nucleotidyltransferase, Transferase, DNA-BINDING PROTEIN, DNA BINDING PROTEIN ;; DNA BINDING PROTEIN
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.

3k75__assembly_1__model_1

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

Download this curve (.dat)

3k75__assembly_1__model_1 | I(q)

10-2 10-1 105 106 107 q (1/Angstrom) I(q)
100 plotted points; both axes use logarithmic scales.

3k75__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）28.13 Å
Rg (electron density)27.51 Å
Total Rg28.14 Å
Atom count3163
Residues399
Excluded volume55790 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3k75__assembly_1__model_1 dimeric （2） Success 4.1.3-1-20251215 (887e7ef) View Download
2 1 3k75__assembly_2__model_1 dimeric （2） 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 (2)

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (7 domains)

Domain ID domain_idd3k75b_
Class classb — All beta proteins
Fold Fold foldb.18 — Galactose-binding domain-like
Superfamily Superfamily superfamilyb.18.1 — Galactose-binding domain-like
Family Family familyb.18.1.8 — N-terminal domain of xrcc1
Domain ID domain_idd3k75c_
Class classb — All beta proteins
Fold Fold foldb.18 — Galactose-binding domain-like
Superfamily Superfamily superfamilyb.18.1 — Galactose-binding domain-like
Family Family familyb.18.1.8 — N-terminal domain of xrcc1
Domain ID domain_idd3k75d1
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.12 — PsbU/PolX domain-like
Family Family familya.60.12.1 — DNA polymerase beta-like, second domain
Domain ID domain_idd3k75d2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.218 — Nucleotidyltransferase
Superfamily Superfamily superfamilyd.218.1 — Nucleotidyltransferase
Family Family familyd.218.1.2 — DNA polymerase beta-like
Domain ID domain_idd3k75d3
Class classl — Artifacts
Fold Fold foldl.1 — Tags
Superfamily Superfamily superfamilyl.1.1 — Tags
Family Family familyl.1.1.1 — Tags
Domain ID domain_idd3k75e1
Class classa — All alpha proteins
Fold Fold folda.60 — SAM domain-like
Superfamily Superfamily superfamilya.60.12 — PsbU/PolX domain-like
Family Family familya.60.12.1 — DNA polymerase beta-like, second domain
Domain ID domain_idd3k75e2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.218 — Nucleotidyltransferase
Superfamily Superfamily superfamilyd.218.1 — Nucleotidyltransferase
Family Family familyd.218.1.2 — DNA polymerase beta-like

CATH v4.4 (8 domains)

Domain ID domain_id3k75B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id3k75C00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology120 — Jelly Rolls
Homologous superfamily homologous superfamily260 — Galactose-binding domain-like
Domain ID domain_id3k75D01
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_id3k75D02
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_id3k75D03
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_id3k75E01
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_id3k75E02
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_id3k75E03
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)