3cwu

Crystal Structure of an AlkA Host/Guest Complex 2'-fluoro-2'-deoxy-1,N6-ethenoadenine:Thymine 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

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	;DNA (5'-D(DGPDAPDCPDAPDTPDGPDAP(2FE)PDTPDGPDCPDC)-3') ; × 2 ;DNA (5'-D(DGPDGPDCPDAPDTPDTPDCPDAPDTPDGPDTPDC)-3') ; × 2 water × 5	Consistent with all polymers

Other States of the Same Protein in the Database

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_id	3cwu
Deposition date deposition_date	2008-04-22
Structure title title	Crystal Structure of an AlkA Host/Guest Complex 2'-fluoro-2'-deoxy-1,N6-ethenoadenine:Thymine Base Pair
Keywords keywords	;AlkA, 2'-fluoro-2'-deoxy-1, N6-ethenoadenine, DNA repair, host-guest complex, DNA structure, DNA damage, Hydrolase, hydrolase-DNA COMPLEX ;; hydrolase/DNA
Experimental Method method	X-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.

3cwu__assembly_1__model_1

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

Download this curve (.dat)

3cwu__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cwu__assembly_1__model_1 | P(r) · Pending

P(r) will be calculated and displayed separately for the same assembly/model.

Rg（Guinier）	36.68 Å
Rg (electron density)	36.43 Å
Total Rg	36.76 Å
Atom count	9838
Residues	1174
Excluded volume	172800 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cwu__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)

Entity 1 Entity 1 polymer

Description description	DNA-3-methyladenine glycosylase 2
Molecular weight formula_weight	31425.2 kDa
EC 编号 ec_number	3.2.2.21
Source method src_method	man
Copy count entity_count	4

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	9875

MYTLNWQPPYDWSWMLGFLAARAVSSVETVADSYYARSLAVGEYRGVVTAIPDIARHTLHINLSAGLEPVAAECLAKMSRLFDLQCNPQIVNGALGRLGAARPGLRLPGCVDAFEQGVRAILGQLVSVAMAAKLTARVAQLYGERLDDFPEYICFPTPQRLAAADPQALKALGMPLKRAEALIHLANAALEGTLPMTIPGDVEQAMKTLQTFPGIGRWTANYFALRGWQAKDVFLPDDYLIKQRFPGMTPAQIRRYAERWKPWRSYALLHIWYTEGWQPDEA

Source Source

Source organism organism	Escherichia coli
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(DGPDAPDCPDAPDTPDGPDAP(2FE)PDTPDGPDCPDC)-3') ;
Molecular weight formula_weight	3713.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,G

GACATGANTGCC

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(DGPDGPDCPDAPDTPDTPDCPDAPDTPDGPDTPDC)-3') ;
Molecular weight formula_weight	3653.4 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	F,H

GGCATTCATGTC

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	37

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d3cwua1
Class class	a — All alpha proteins
Fold Fold fold	a.96 — DNA-glycosylase
Superfamily Superfamily superfamily	a.96.1 — DNA-glycosylase
Family Family family	a.96.1.3 — DNA repair glycosylase, 2 C-terminal domains

Domain ID domain_id	d3cwua2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.2 — DNA repair glycosylase, N-terminal domain

Domain ID domain_id	d3cwub1
Class class	a — All alpha proteins
Fold Fold fold	a.96 — DNA-glycosylase
Superfamily Superfamily superfamily	a.96.1 — DNA-glycosylase
Family Family family	a.96.1.3 — DNA repair glycosylase, 2 C-terminal domains

Domain ID domain_id	d3cwub2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.2 — DNA repair glycosylase, N-terminal domain

Domain ID domain_id	d3cwuc1
Class class	a — All alpha proteins
Fold Fold fold	a.96 — DNA-glycosylase
Superfamily Superfamily superfamily	a.96.1 — DNA-glycosylase
Family Family family	a.96.1.3 — DNA repair glycosylase, 2 C-terminal domains

Domain ID domain_id	d3cwuc2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.2 — DNA repair glycosylase, N-terminal domain

Domain ID domain_id	d3cwud1
Class class	a — All alpha proteins
Fold Fold fold	a.96 — DNA-glycosylase
Superfamily Superfamily superfamily	a.96.1 — DNA-glycosylase
Family Family family	a.96.1.3 — DNA repair glycosylase, 2 C-terminal domains

Domain ID domain_id	d3cwud2
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.129 — TBP-like
Superfamily Superfamily superfamily	d.129.1 — TATA-box binding protein-like
Family Family family	d.129.1.2 — DNA repair glycosylase, N-terminal domain

CATH v4.4 (12 domains)

Domain ID domain_id	3cwuA01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	20 — DNA-3-methyladenine glycosylase AlkA, N-terminal domain

Domain ID domain_id	3cwuA02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily	30 — Hypothetical protein; domain 2

Domain ID domain_id	3cwuA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily	10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)

Domain ID domain_id	3cwuB01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	20 — DNA-3-methyladenine glycosylase AlkA, N-terminal domain

Domain ID domain_id	3cwuB02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily	30 — Hypothetical protein; domain 2

Domain ID domain_id	3cwuB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily	10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)

Domain ID domain_id	3cwuC01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	20 — DNA-3-methyladenine glycosylase AlkA, N-terminal domain

Domain ID domain_id	3cwuC02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily	30 — Hypothetical protein; domain 2

Domain ID domain_id	3cwuC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily	10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)

Domain ID domain_id	3cwuD01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	310 — TATA-Binding Protein
Homologous superfamily homologous superfamily	20 — DNA-3-methyladenine glycosylase AlkA, N-terminal domain

Domain ID domain_id	3cwuD02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	340 — Endonuclease III; domain 1
Homologous superfamily homologous superfamily	30 — Hypothetical protein; domain 2

Domain ID domain_id	3cwuD03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	1670 — Endonuclease Iii, domain 2
Homologous superfamily homologous superfamily	10 — Helix-hairpin-Helix base-excision DNA repair enzymes (C-terminal)

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Unit-cell length a length_a	74.938 Å
Unit-cell length b length_b	100.742 Å
Unit-cell length c length_c	102.978 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.86 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	—
R_work r_work	0.2130
R_free r_free	0.2730

Crystal Structure of an AlkA Host/Guest Complex 2'-fluoro-2'-deoxy-1,N6-ethenoadenine:Thymine Base Pair

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-3-methyladenine glycosylase 2

State in the Current Structure

Other States of the Same Protein in the Database

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3cwu__assembly_1__model_1

3cwu__assembly_1__model_1 | I(q)

3cwu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)

Crystal Structure of an AlkA Host/Guest Complex 2'-fluoro-2'-deoxy-1,N6-ethenoadenine:Thymine Base Pair

1. Protein Identity and Related Structures Protein Identity & Related Structures

DNA-3-methyladenine glycosylase 2

State in the Current Structure

Other States of the Same Protein in the Database

Monomer

Homodimer

Homotetramer

Other homooligomers

Heteromeric or nucleic-acid complex

2. Structure Basics 2. Structure Basics

3. Official assembly/model SAXS Official SAXS Profiles

3cwu__assembly_1__model_1

3cwu__assembly_1__model_1 | I(q)

3cwu__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

5. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (8 domains)

CATH v4.4 (12 domains)

7. Citations (1)