SAXSdb — 3khc

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

Alpha-ketoglutarate-dependent dioxygenase alkB

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein–DNA	Homooligomer	Protein 2 DNA 2	;DNA (5'-D(PTPAP(MG1)PTPGPCPCPT)-3') ; × 1 ;DNA (5'-D(PGPCPAPT)-3') ; × 1 COBALT (II) ION × 2 2-OXOGLUTARIC ACID × 2 water × 4	Consistent with all polymers

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	ALKB_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–219； UniProt 1–216 Author chain B； PDBConstruct 4–219； UniProt 1–216

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	3khc
Deposition date deposition_date	2009-10-30
Structure title title	Crystal Structure of Escherichia coli AlkB in complex with ssDNA containing a 1-methylguanine lesion
Keywords keywords	;oxidoreductase, 1-methylguanine, AlkB, 2-oxoglutarate, Dioxygenase, DNA damage, DNA repair, Iron, Metal-binding, oxidoreductase-DNA complex ;; oxidoreductase/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.

3khc__assembly_1__model_1

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

Download this curve (.dat)

3khc__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3khc__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	25.83 Å
Rg (electron density)	25.17 Å
Total Rg	25.92 Å
Atom count	3511
Residues	425
Excluded volume	61548 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3khc__assembly_1__model_1`	tetrameric （4）	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	Alpha-ketoglutarate-dependent dioxygenase alkB
Molecular weight formula_weight	24351.8 kDa
EC 编号 ec_number	1.14.11.-
Mutation mutation	D135A
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3833

GPHMLDLFADAEPWQEPLAAGAVILRRFAFNAAEQLIRDINDVASQSPFRQMVTPGGYTMSVAMTNCGHLGWTTHRQGYLYSPIDPQTNKPWPAMPQSFHNLCQRAATAAGYPDFQPDACLINRYAPGAKLSLHQDKAEPDLRAPIVSVSLGLPAIFQFGGLKRNDPLKRLLLEHGDVVVWGGESRLFYHGIQPLKAGFHPLTIDCRYNLTFRQAGKKE

Source Source

Source organism organism	Escherichia coli K-12
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	;DNA (5'-D(PTPAP(MG1)PTPGPCPCPT)-3') ;
Molecular weight formula_weight	2431.6 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	C

TAGTGCCT

Entity 3 Entity 3 polymer

Description description	;DNA (5'-D(PGPCPAPT)-3') ;
Molecular weight formula_weight	1190.8 kDa
Source method src_method	syn
Copy count entity_count	1

Polymer Polymer

Polymer type type	polydeoxyribonucleotide
Chain IDs strand_id	D

GCAT

Entity 4 Entity 4 non-polymer

Description description	COBALT (II) ION
Molecular weight formula_weight	58.9 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 5 Entity 5 non-polymer

Description description	2-OXOGLUTARIC ACID
Molecular weight formula_weight	146.1 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	269

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d3khca_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.10 — AlkB-like

Domain ID domain_id	d3khcb_
Class class	b — All beta proteins
Fold Fold fold	b.82 — Double-stranded beta-helix
Superfamily Superfamily superfamily	b.82.2 — Clavaminate synthase-like
Family Family family	b.82.2.10 — AlkB-like

CATH v4.4 (2 domains)

Domain ID domain_id	3khcA00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	590 — Alpha-ketoglutarate-dependent dioxygenase AlkB-like

Domain ID domain_id	3khcB00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	120 — Jelly Rolls
Homologous superfamily homologous superfamily	590 — Alpha-ketoglutarate-dependent dioxygenase AlkB-like

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Unit-cell length a length_a	147.809 Å
Unit-cell length b length_b	41.441 Å
Unit-cell length c length_c	85.622 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	120.98 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	23.740 Å
R factor r_factor	0.2143
R_work r_work	0.2113
R_free r_free	0.2733

Crystal Structure of Escherichia coli AlkB in complex with ssDNA containing a 1-methylguanine lesion

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

Alpha-ketoglutarate-dependent dioxygenase alkB

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

3khc__assembly_1__model_1

3khc__assembly_1__model_1 | I(q)

3khc__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

Crystal Structure of Escherichia coli AlkB in complex with ssDNA containing a 1-methylguanine lesion

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

Alpha-ketoglutarate-dependent dioxygenase alkB

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

3khc__assembly_1__model_1

3khc__assembly_1__model_1 | I(q)

3khc__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) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)