SAXSdb — 5kn8

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

Adenine DNA glycosylase

Geobacillus stearothermophilus

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	;DNA (5'-D(APTPCPCPTPGPTPGPCPT)-3') ; × 1 ;DNA (5'-D(APGPCPAPCPAPGPGPAPT)-3') ; × 1 IRON/SULFUR CLUSTER × 1 CALCIUM ION × 1 water × 3	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	MUTY_GEOSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–232； UniProt 1–229

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	5kn8
Deposition date deposition_date	2016-06-27
Structure title title	MutY N-terminal domain in complex with undamaged DNA
Keywords keywords	adenine glycosylase, oxoG, DNA repair protein, lesion-scanning complex, 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.

5kn8__assembly_1__model_1

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

Download this curve (.dat)

5kn8__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5kn8__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	19.63 Å
Rg (electron density)	18.62 Å
Total Rg	19.49 Å
Atom count	2203
Residues	242
Excluded volume	38114 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5kn8__assembly_1__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 (6)

Entity 1 Entity 1 polymer

Description description	Adenine DNA glycosylase
Molecular weight formula_weight	26630.4 kDa
EC 编号 ec_number	3.2.2.-
Mutation mutation	D144N, P164C
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2422

GSHMTRETERFPAREFQRDLLDWFARERRDLPWRKDRDPYKVWVSEVMLQQTRVETVIPYFEQFIDRFPTLEALADADEDEVLKAWEGLGYYSRVRNLHAAVKEVKTRYGGKVPDDPDEFSRLKGVGPYTVGAVLSLAYGVPEPAVNGNVMRVLSRLFLVTDDIAKCSTRKRFEQIVREIMAYENPGAFNEALIELGALVCTPRRPSCLLCPVQAYCQAFAEGVAEELPVKM

Source Source

Source organism organism	Geobacillus stearothermophilus
NCBI taxonomy ID ncbi_taxonomy_id	1422
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(APTPCPCPTPGPTPGPCPT)-3') ;
Molecular weight formula_weight	3011.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

ATCCTGTGCT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(APGPCPAPCPAPGPGPAPT)-3') ;
Molecular weight formula_weight	3078.0 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

AGCACAGGAT

Entity 4 Entity 4 non-polymer

Description description	IRON/SULFUR CLUSTER
Molecular weight formula_weight	351.6 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	CALCIUM ION
Molecular weight formula_weight	40.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	182

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	5kn8A01
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	5kn8A02
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

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Unit-cell length a length_a	49.200 Å
Unit-cell length b length_b	38.618 Å
Unit-cell length c length_c	83.796 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	104.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	2

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

Resolution resolution	1.810 Å
Low-resolution limit resolution_low	46.354 Å
R factor r_factor	0.1692
R_work r_work	0.1665
R_free r_free	0.2196

MutY N-terminal domain in complex with undamaged DNA

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

Adenine 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

5kn8__assembly_1__model_1

5kn8__assembly_1__model_1 | I(q)

5kn8__assembly_1__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

MutY N-terminal domain in complex with undamaged DNA

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

Adenine 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

5kn8__assembly_1__model_1

5kn8__assembly_1__model_1 | I(q)

5kn8__assembly_1__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 (6)

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 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)