1k82

Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA

Method: X-RAY DIFFRACTION

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

formamidopyrimidine-DNA glycosylase

Escherichia coli

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	5'-D(GPGPCPTPTPCPCPTPCPCPTPGPG)-3' × 1 5'-D(CPCPAPGPGPAP(PED)PGPAPAPGPCPC)-3' × 1 ZINC ION × 1 water × 3	Consistent with all polymers
2	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(GPGPCPTPTPCPCPTPCPCPTPGPG)-3' × 1 5'-D(CPCPAPGPGPAP(PED)PGPAPAPGPCPC)-3' × 1 ZINC ION × 1 water × 3	Consistent with all polymers
3	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(GPGPCPTPTPCPCPTPCPCPTPGPG)-3' × 1 5'-D(CPCPAPGPGPAP(PED)PGPAPAPGPCPC)-3' × 1 ZINC ION × 1 water × 3	Consistent with all polymers
4	Protein–DNA	Monomer	Protein 1 DNA 2	5'-D(GPGPCPTPTPCPCPTPCPCPTPGPG)-3' × 1 5'-D(CPCPAPGPGPAP(PED)PGPAPAPGPCPC)-3' × 1 ZINC ION × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	FPG_ECOLI
Isoform	—
PDB entities	3
Chains and sequence ranges	Author chain A； PDBConstruct 1–268； UniProt 2–269 Author chain B； PDBConstruct 1–268； UniProt 2–269 Author chain C； PDBConstruct 1–268； UniProt 2–269 Author chain D； PDBConstruct 1–268； UniProt 2–269

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	1k82
Deposition date deposition_date	2001-10-22
Structure title title	Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA
Keywords keywords	PROTEIN-DNA COMPLEX, DNA REPAIR, BETA SANDWICH, ZINC FINGER, HELIX TWO-TURNS HELIX, 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.

1k82__assembly_4__model_1

Assembly 4 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

1k82__assembly_4__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1k82__assembly_4__model_1 | P(r) · Pending

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

Rg（Guinier）	20.93 Å
Rg (electron density)	20.08 Å
Total Rg	20.92 Å
Atom count	2556
Residues	285
Excluded volume	44039 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1k82__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1k82__assembly_2__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`1k82__assembly_3__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`1k82__assembly_4__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 (5)

Entity 1 Entity 1 polymer

Description description	5'-D(GPGPCPTPTPCPCPTPCPCPTPGP*G)-3'
Molecular weight formula_weight	3934.5 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	E,F,G,H
Atom count atom_count	10716

GGCTTCCTCCTGG

Entity 2 Entity 2 polymer

Description description	5'-D(CPCPAPGPGPAP(PED)PGPAPAPGPCP*C)-3'
Molecular weight formula_weight	3863.5 kDa
Source method src_method	syn
Copy count entity_count	4

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	I,J,K,L

CCAGGAXGAAGCC

Entity 3 Entity 3 polymer

Description description	formamidopyrimidine-DNA glycosylase
Molecular weight formula_weight	30203.9 kDa
EC 编号 ec_number	3.2.2.23
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

PELPEVETSRRGIEPHLVGATILHAVVRNGRLRWPVSEEIYRLSDQPVLSVQRRAKYLLLELPEGWIIIHLGMSGSLRILPEELPPEKHDHVDLVMSNGKVLRYTDPRRFGAWLWTKELEGHNVLTHLGPEPLSDDFNGEYLHQKCAKKKTAIKPWLMDNKLVVGVGNIYASESLFAAGIHPDRLASSLSLAECELLARVIKAVLLRSIEQGGTTLKDFLQSDGKPGYFAQELQVYGRKGEPCRVCGTPIVATKHAQRATFYCRQCQK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	562
Host organism host_organism	Escherichia coli

Entity 4 Entity 4 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	499

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6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1k82a1
Class class	a — All alpha proteins
Fold Fold fold	a.156 — S13-like H2TH domain
Superfamily Superfamily superfamily	a.156.1 — S13-like H2TH domain
Family Family family	a.156.1.2 — Middle domain of MutM-like DNA repair proteins

Domain ID domain_id	d1k82a2
Class class	b — All beta proteins
Fold Fold fold	b.113 — N-terminal domain of MutM-like DNA repair proteins
Superfamily Superfamily superfamily	b.113.1 — N-terminal domain of MutM-like DNA repair proteins
Family Family family	b.113.1.1 — N-terminal domain of MutM-like DNA repair proteins

Domain ID domain_id	d1k82a3
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.8 — C-terminal, Zn-finger domain of MutM-like DNA repair proteins

Domain ID domain_id	d1k82b1
Class class	a — All alpha proteins
Fold Fold fold	a.156 — S13-like H2TH domain
Superfamily Superfamily superfamily	a.156.1 — S13-like H2TH domain
Family Family family	a.156.1.2 — Middle domain of MutM-like DNA repair proteins

Domain ID domain_id	d1k82b2
Class class	b — All beta proteins
Fold Fold fold	b.113 — N-terminal domain of MutM-like DNA repair proteins
Superfamily Superfamily superfamily	b.113.1 — N-terminal domain of MutM-like DNA repair proteins
Family Family family	b.113.1.1 — N-terminal domain of MutM-like DNA repair proteins

Domain ID domain_id	d1k82b3
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.8 — C-terminal, Zn-finger domain of MutM-like DNA repair proteins

Domain ID domain_id	d1k82c1
Class class	a — All alpha proteins
Fold Fold fold	a.156 — S13-like H2TH domain
Superfamily Superfamily superfamily	a.156.1 — S13-like H2TH domain
Family Family family	a.156.1.2 — Middle domain of MutM-like DNA repair proteins

Domain ID domain_id	d1k82c2
Class class	b — All beta proteins
Fold Fold fold	b.113 — N-terminal domain of MutM-like DNA repair proteins
Superfamily Superfamily superfamily	b.113.1 — N-terminal domain of MutM-like DNA repair proteins
Family Family family	b.113.1.1 — N-terminal domain of MutM-like DNA repair proteins

Domain ID domain_id	d1k82c3
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.8 — C-terminal, Zn-finger domain of MutM-like DNA repair proteins

Domain ID domain_id	d1k82d1
Class class	a — All alpha proteins
Fold Fold fold	a.156 — S13-like H2TH domain
Superfamily Superfamily superfamily	a.156.1 — S13-like H2TH domain
Family Family family	a.156.1.2 — Middle domain of MutM-like DNA repair proteins

Domain ID domain_id	d1k82d2
Class class	b — All beta proteins
Fold Fold fold	b.113 — N-terminal domain of MutM-like DNA repair proteins
Superfamily Superfamily superfamily	b.113.1 — N-terminal domain of MutM-like DNA repair proteins
Family Family family	b.113.1.1 — N-terminal domain of MutM-like DNA repair proteins

Domain ID domain_id	d1k82d3
Class class	g — Small proteins
Fold Fold fold	g.39 — Glucocorticoid receptor-like (DNA-binding domain)
Superfamily Superfamily superfamily	g.39.1 — Glucocorticoid receptor-like (DNA-binding domain)
Family Family family	g.39.1.8 — C-terminal, Zn-finger domain of MutM-like DNA repair proteins

CATH v4.4 (8 domains)

Domain ID domain_id	1k82A01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	190 — N-terminal domain of MutM-like DNA repair proteins
Homologous superfamily homologous superfamily	10 — MutM-like, N-terminal

Domain ID domain_id	1k82A02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1k82B01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	190 — N-terminal domain of MutM-like DNA repair proteins
Homologous superfamily homologous superfamily	10 — MutM-like, N-terminal

Domain ID domain_id	1k82B02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1k82C01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	190 — N-terminal domain of MutM-like DNA repair proteins
Homologous superfamily homologous superfamily	10 — MutM-like, N-terminal

Domain ID domain_id	1k82C02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 —

Domain ID domain_id	1k82D01
Class class	3 — Alpha Beta
Architecture architecture	20 — Alpha-Beta Barrel
Topology topology	190 — N-terminal domain of MutM-like DNA repair proteins
Homologous superfamily homologous superfamily	10 — MutM-like, N-terminal

Domain ID domain_id	1k82D02
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	8 — Helicase, Ruva Protein; domain 3
Homologous superfamily homologous superfamily	50 —

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Unit-cell length a length_a	80.704 Å
Unit-cell length b length_b	96.033 Å
Unit-cell length c length_c	96.228 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	96.80 °
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	2.100 Å
Low-resolution limit resolution_low	34.000 Å
R factor r_factor	—
R_work r_work	0.2140
R_free r_free	0.2650

Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA

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

formamidopyrimidine-DNA glycosylase

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

1k82__assembly_4__model_1

1k82__assembly_4__model_1 | I(q)

1k82__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal structure of E.coli formamidopyrimidine-DNA glycosylase (Fpg) covalently trapped with DNA

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

formamidopyrimidine-DNA glycosylase

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

1k82__assembly_4__model_1

1k82__assembly_4__model_1 | I(q)

1k82__assembly_4__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

5. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 polymer

Polymer Polymer

Source Source

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 20 domains

SCOP 2.08 (12 domains)

CATH v4.4 (8 domains)

7. Citations (1)