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3d4v

Crystal Structure of an AlkA Host/Guest Complex N7MethylGuanine:Cytosine Base Pair

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

DNA-3-methyladenine glycosylase 2

Escherichia coli

UniProt P04395

State in the Current Structure

Assembly Physical composition Protein state Molecular copy count Associated components Data consistency
1 Protein–DNA Homooligomer Protein 4 DNA 4 5'-D(*DGP*DAP*DCP*DAP*DTP*DGP*DAP*(FMG)P*DTP*DGP*DCP*DC)-3' × 2 5'-D(*DGP*DGP*DCP*DAP*DCP*DTP*DCP*DAP*DTP*DGP*DTP*DC)-3' × 2 water × 5 Consistent with all polymers

Other States of the Same Protein in the Database

Monomer
1mpg 1mpg 1pvs 1pvs

4 assemblies

Homodimer

None

Homotetramer

None

Other homooligomers

None

Heteromeric or nucleic-acid complex
1diz 1diz 3cvs 3cvt 3cw7 3cwa 3cws 3cwt 3cwu 3d4v 3ogd 3oh6

14 assemblies; showing the first 12

View Construct and Data Evidence
UniProt name 3MG2_ECOLI
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 1–282； UniProt 1–282 Author chain B； PDBConstruct 1–282； UniProt 1–282 Author chain C； PDBConstruct 1–282； UniProt 1–282 Author chain D； PDBConstruct 1–282； UniProt 1–282

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_id3d4v
Deposition date deposition_date2008-05-15
Structure title titleCrystal Structure of an AlkA Host/Guest Complex N7MethylGuanine:Cytosine Base Pair
Keywords keywordsAlkA, N7MethylGuanine, DNA repair, host-guest complex, DNA structure, DNA damage, Hydrolase, HYDROLASE-DNA COMPLEX; HYDROLASE/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.

3d4v__assembly_1__model_1

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

Download this curve (.dat)

3d4v__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.

3d4v__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）36.43 Å
Rg (electron density)36.16 Å
Total Rg36.49 Å
Atom count9824
Residues1172
Excluded volume172560 ų
Maximum q0.500 Å⁻¹
Assembly Model Structure unit Oligomeric description Status CRYSOL Actions
1 1 3d4v__assembly_1__model_1 octameric （8） 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 (4)

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd3d4va1
Class classa — All alpha proteins
Fold Fold folda.96 — DNA-glycosylase
Superfamily Superfamily superfamilya.96.1 — DNA-glycosylase
Family Family familya.96.1.3 — DNA repair glycosylase, 2 C-terminal domains
Domain ID domain_idd3d4va2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.2 — DNA repair glycosylase, N-terminal domain
Domain ID domain_idd3d4vb1
Class classa — All alpha proteins
Fold Fold folda.96 — DNA-glycosylase
Superfamily Superfamily superfamilya.96.1 — DNA-glycosylase
Family Family familya.96.1.3 — DNA repair glycosylase, 2 C-terminal domains
Domain ID domain_idd3d4vb2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.2 — DNA repair glycosylase, N-terminal domain
Domain ID domain_idd3d4vc1
Class classa — All alpha proteins
Fold Fold folda.96 — DNA-glycosylase
Superfamily Superfamily superfamilya.96.1 — DNA-glycosylase
Family Family familya.96.1.3 — DNA repair glycosylase, 2 C-terminal domains
Domain ID domain_idd3d4vc2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.2 — DNA repair glycosylase, N-terminal domain
Domain ID domain_idd3d4vd1
Class classa — All alpha proteins
Fold Fold folda.96 — DNA-glycosylase
Superfamily Superfamily superfamilya.96.1 — DNA-glycosylase
Family Family familya.96.1.3 — DNA repair glycosylase, 2 C-terminal domains
Domain ID domain_idd3d4vd2
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.129 — TBP-like
Superfamily Superfamily superfamilyd.129.1 — TATA-box binding protein-like
Family Family familyd.129.1.2 — DNA repair glycosylase, N-terminal domain

CATH v4.4 (12 domains)

Domain ID domain_id3d4vA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily20 — DNA-3-methyladenine glycosylase AlkA, N-terminal domain
Domain ID domain_id3d4vA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily30 — Hypothetical protein; domain 2
Domain ID domain_id3d4vA03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)
Domain ID domain_id3d4vB01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily20 — DNA-3-methyladenine glycosylase AlkA, N-terminal domain
Domain ID domain_id3d4vB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily30 — Hypothetical protein; domain 2
Domain ID domain_id3d4vB03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)
Domain ID domain_id3d4vC01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily20 — DNA-3-methyladenine glycosylase AlkA, N-terminal domain
Domain ID domain_id3d4vC02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily30 — Hypothetical protein; domain 2
Domain ID domain_id3d4vC03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)
Domain ID domain_id3d4vD01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology310 — TATA-Binding Protein
Homologous superfamily homologous superfamily20 — DNA-3-methyladenine glycosylase AlkA, N-terminal domain
Domain ID domain_id3d4vD02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily30 — Hypothetical protein; domain 2
Domain ID domain_id3d4vD03
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)
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7. Citations (1)