SAXSdb — 3pnl

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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 heterocomplex	Heteromer	Protein 4	PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL × 2 （P76014） GLYCEROL × 2 ADENOSINE-5'-DIPHOSPHATE × 2 MAGNESIUM ION × 4 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL × 1 （P76014） GLYCEROL × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 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

PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL

Escherichia coli

UniProt P76014

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein heterocomplex	Heteromer	Protein 4	PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK × 2 （P76015） GLYCEROL × 2 ADENOSINE-5'-DIPHOSPHATE × 2 MAGNESIUM ION × 4 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK × 1 （P76015） GLYCEROL × 1 ADENOSINE-5'-DIPHOSPHATE × 1 MAGNESIUM ION × 2 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHAL_ECOLI
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 3–211； UniProt 2–210

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	3pnl
Deposition date deposition_date	2010-11-19
Structure title title	Crystal Structure of E.coli Dha kinase DhaK-DhaL complex
Keywords keywords	Structural Genomics, Montreal-Kingston Bacterial Structural Genomics Initiative, BSGI, Dha kinase, 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.

3pnl__assembly_2__model_1

Assembly 2 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3pnl__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3pnl__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	24.67 Å
Rg (electron density)	23.85 Å
Total Rg	24.61 Å
Atom count	4290
Residues	567
Excluded volume	75850 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3pnl__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3pnl__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 (6)

Entity 1 Entity 1 polymer

Description description	PTS-dependent dihydroxyacetone kinase, dihydroxyacetone-binding subunit dhaK
Molecular weight formula_weight	38264.0 kDa
EC 编号 ec_number	2.7.-.-
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	4491

GSKKLINDVQDVLDEQLAGLAKAHPSLTLHQDPVYVTRADAPVAGKVALLSGGGSGHEPMHCGYIGQGMLSGACPGEIFTSPTPDKIFECAMQVDGGEGVLLIIKNYTGDILNFETATELLHDSGVKVTTVVIDDDVAVKDSLYTAGRRGVANTVLIEKLVGAAAERGDSLDACAELGRKLNNQGHSIGIALGACTVPAAGKPSFTLADNEMEFGVGIHGEPGIDRRPFSSLDQTVDEMFDTLLVNGSYHRTLRFWDYQQGSWQEEQQTKQPLQSGDRVIALVNNLGATPLSELYGVYNRLTTRCQQAGLTIERNLIGAYCTSLDMTGFSITLLKVDDETLALWDAPVHTPALNWGK

Source Source

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

Entity 2 Entity 2 polymer

Description description	PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL
Molecular weight formula_weight	22666.7 kDa
EC 编号 ec_number	2.7.-.-
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

GSSLSRTQIVNWLTRCGDIFSTESEYLTGLDREIGDADHGLNMNRGFSKVVEKLPAIADKDIGFILKNTGMTLLSSVGGASGPLFGTFFIRAAQATQARQSLTLEELYQMFRDGADGVISRGKAEPGDKTMCDVWVPVVESLRQSSEQNLSVPVALEAASSIAESAAQSTITMQARKGRASYLGERSIGHQDPGATSVMFMMQMLALAAKE

Source Source

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

Entity 3 Entity 3 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 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	196

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6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3pnla1
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	d3pnla2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

Domain ID domain_id	d3pnlb1
Class class	a — All alpha proteins
Fold Fold fold	a.208 — DhaL-like
Superfamily Superfamily superfamily	a.208.1 — DhaL-like
Family Family family	a.208.1.0 — automated matches

Domain ID domain_id	d3pnlb2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (3 domains)

Domain ID domain_id	3pnlA01
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	3pnlA02
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	3pnlB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	340 — DhaL domain

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Unit-cell length a length_a	74.572 Å
Unit-cell length b length_b	74.572 Å
Unit-cell length c length_c	268.779 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 41 21 2
Space-group number int_tables_number	92
Crystal system crystal_system	—

Resolution resolution	2.200 Å
Low-resolution limit resolution_low	49.920 Å
R factor r_factor	0.1911
R_work r_work	0.1893
R_free r_free	0.2248

Crystal Structure of E.coli Dha kinase DhaK-DhaL complex

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

PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL

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

3pnl__assembly_2__model_1

3pnl__assembly_2__model_1 | I(q)

3pnl__assembly_2__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)

Crystal Structure of E.coli Dha kinase DhaK-DhaL complex

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

PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL

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

3pnl__assembly_2__model_1

3pnl__assembly_2__model_1 | I(q)

3pnl__assembly_2__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

Source Source

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 7 domains

SCOP 2.08 (4 domains)

CATH v4.4 (3 domains)

7. Citations (1)