3pno

Crystal Structure of E.coli Dha kinase DhaK (H56N)

Method: X-RAY DIFFRACTION

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

PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK

Escherichia coli

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHAK_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 3–357； UniProt 2–356 Author chain B； PDBConstruct 3–357； UniProt 2–356 Author chain C； PDBConstruct 3–357； UniProt 2–356 Author chain D； PDBConstruct 3–357； UniProt 2–356

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	3pno
Deposition date deposition_date	2010-11-19
Structure title title	Crystal Structure of E.coli Dha kinase DhaK (H56N)
Keywords keywords	Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, TRANSFERASE; TRANSFERASE
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.

3pno__assembly_1__model_1

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

Download this curve (.dat)

3pno__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pno__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	26.48 Å
Rg (electron density)	25.26 Å
Total Rg	25.97 Å
Atom count	5064
Residues	672
Excluded volume	89511 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pno__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pno__assembly_2__model_1`	dimeric （2）	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 (2)

Entity 1 Entity 1 polymer

Description description	PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
Molecular weight formula_weight	38239.9 kDa
EC 编号 ec_number	2.7.-.-
Mutation mutation	H56N
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	11284

GSKKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGNEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK

Source Source

Source organism organism	Escherichia coli
NCBI taxonomy ID ncbi_taxonomy_id	83333
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1018

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6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3pnoa_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.119 — DAK1/DegV-like
Superfamily Superfamily superfamily	c.119.1 — DAK1/DegV-like
Family Family family	c.119.1.2 — DAK1

Domain ID domain_id	d3pnob_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.119 — DAK1/DegV-like
Superfamily Superfamily superfamily	c.119.1 — DAK1/DegV-like
Family Family family	c.119.1.2 — DAK1

Domain ID domain_id	d3pnoc_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.119 — DAK1/DegV-like
Superfamily Superfamily superfamily	c.119.1 — DAK1/DegV-like
Family Family family	c.119.1.2 — DAK1

Domain ID domain_id	d3pnod_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.119 — DAK1/DegV-like
Superfamily Superfamily superfamily	c.119.1 — DAK1/DegV-like
Family Family family	c.119.1.2 — DAK1

CATH v4.4 (8 domains)

Domain ID domain_id	3pnoA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10440 — Dihydroxyacetone kinase; domain 1

Domain ID domain_id	3pnoA02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1180 — Hypothetical Protein Tm841; Chain: A;domain 3
Homologous superfamily homologous superfamily	20 — Dihydroxyacetone kinase; domain 2

Domain ID domain_id	3pnoB01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10440 — Dihydroxyacetone kinase; domain 1

Domain ID domain_id	3pnoB02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1180 — Hypothetical Protein Tm841; Chain: A;domain 3
Homologous superfamily homologous superfamily	20 — Dihydroxyacetone kinase; domain 2

Domain ID domain_id	3pnoC01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10440 — Dihydroxyacetone kinase; domain 1

Domain ID domain_id	3pnoC02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1180 — Hypothetical Protein Tm841; Chain: A;domain 3
Homologous superfamily homologous superfamily	20 — Dihydroxyacetone kinase; domain 2

Domain ID domain_id	3pnoD01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10440 — Dihydroxyacetone kinase; domain 1

Domain ID domain_id	3pnoD02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	1180 — Hypothetical Protein Tm841; Chain: A;domain 3
Homologous superfamily homologous superfamily	20 — Dihydroxyacetone kinase; domain 2

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Unit-cell length a length_a	59.692 Å
Unit-cell length b length_b	82.561 Å
Unit-cell length c length_c	92.856 Å
Unit-cell angle α angle_alpha	77.91 °
Unit-cell angle β angle_beta	78.14 °
Unit-cell angle γ angle_gamma	71.07 °
Molecules per unit cell Z z_pdb	4

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

Resolution resolution	1.970 Å
Low-resolution limit resolution_low	41.520 Å
R factor r_factor	0.1886
R_work r_work	0.1870
R_free r_free	0.2195

Crystal Structure of E.coli Dha kinase DhaK (H56N)

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

PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK

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

3pno__assembly_1__model_1

3pno__assembly_1__model_1 | I(q)

3pno__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)

Crystal Structure of E.coli Dha kinase DhaK (H56N)

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

PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK

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

3pno__assembly_1__model_1

3pno__assembly_1__model_1 | I(q)

3pno__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 12 domains

SCOP 2.08 (4 domains)

CATH v4.4 (8 domains)

7. Citations (1)