SAXSdb — 3cr3

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

PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL

Lactococcus lactis subsp. lactis

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, phosphotransferase subunit dhaM × 2 （Q9CIV6） MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM × 1 （Q9CIV6） MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM × 1 （Q9CIV6） MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM × 1 （Q9CIV6） MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM × 1 （Q9CIV6） MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHAL_LACLA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 2–192； UniProt 2–192 Author chain B； PDBConstruct 2–192； UniProt 2–192

PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM

Lactococcus lactis subsp. lactis

UniProt Q9CIV6

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 （Q9CIV7） MAGNESIUM ION × 4 ADENOSINE-5'-DIPHOSPHATE × 2 water × 4	Consistent with protein count
2	Protein heterocomplex	Heteromer	Protein 2	PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL × 1 （Q9CIV7） MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count
3	Protein heterocomplex	Heteromer	Protein 2	PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL × 1 （Q9CIV7） MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count
4	Protein heterocomplex	Heteromer	Protein 2	PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL × 1 （Q9CIV7） MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count
5	Protein heterocomplex	Heteromer	Protein 2	PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL × 1 （Q9CIV7） MAGNESIUM ION × 2 ADENOSINE-5'-DIPHOSPHATE × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHAM_LACLA
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 1–121； UniProt 3–123 Author chain D； PDBConstruct 1–121； UniProt 3–123

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	3cr3
Deposition date deposition_date	2008-04-04
Structure title title	Structure of a transient complex between Dha-kinase subunits DhaM and DhaL from Lactococcus lactis
Keywords keywords	;Transient Protein-protein complex TRANSFERASE complex PTS-DEPENDENT DIHYDROXYACETONE KINASE, ATP-binding, Glycerol metabolism, Nucleotide-binding, Phosphotransferase system, 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.

3cr3__assembly_3__model_1

Assembly 3 · Model 1 · CRYSOL 4.1.3-1-20251215 (887e7ef)

Download this curve (.dat)

3cr3__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3cr3__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	20.70 Å
Rg (electron density)	20.20 Å
Total Rg	20.78 Å
Atom count	2392
Residues	302
Excluded volume	42955 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3cr3__assembly_1__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3cr3__assembly_2__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3cr3__assembly_3__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3cr3__assembly_4__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3cr3__assembly_5__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 (5)

Entity 1 Entity 1 polymer

Description description	PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL
Molecular weight formula_weight	20909.6 kDa
EC 编号 ec_number	2.7.-.-
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	4976

LLTIDTTIEWLGKFNEKIQENKAYLSELDGPIGDGDHGANMARGMSETMKALEVSNFGNVSEIFKKVAMTLMSKVGGASGPLYGSAFLAMSKTAIETLDTSELIYAGLEAIQKRGKAQVGEKTMVDIWSAFLNDLQTDSASKDNLEKVVKASAGLLATKGRASYLGERSIGHIDPGTQSSAYLFETLLEVVA

Source Source

Source organism organism	Lactococcus lactis subsp. lactis
Common name common_name	Streptococcus lactis
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM
Molecular weight formula_weight	13360.6 kDa
EC 编号 ec_number	2.7.1.-
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,D

YGIVIVSHSPEIASGLKKLIREVAKNISLTAIGGLENGEIGTSFDRVMNAIEENEADNLLTFFDLGSARMNLDLVSEMTDKELTIFNVPLIEGAYTASALLEAGATFEAIKEQLEKMLIEK

Source Source

Source organism organism	Lactococcus lactis subsp. lactis
Common name common_name	Streptococcus lactis
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	4

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	2

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	192

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d3cr3a1
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.208.1.1 — DhaL-like

Domain ID domain_id	d3cr3b_
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.208.1.1 — DhaL-like

Domain ID domain_id	d3cr3c_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.54 — PTS system fructose IIA component-like
Superfamily Superfamily superfamily	c.54.1 — PTS system fructose IIA component-like
Family Family family	c.54.1.2 — DhaM-like

Domain ID domain_id	d3cr3d_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.54 — PTS system fructose IIA component-like
Superfamily Superfamily superfamily	c.54.1 — PTS system fructose IIA component-like
Family Family family	c.54.1.2 — DhaM-like

CATH v4.4 (4 domains)

Domain ID domain_id	3cr3A00
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

Domain ID domain_id	3cr3B00
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

Domain ID domain_id	3cr3C00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	510 — Phosphotransferase system, mannose-type IIA component

Domain ID domain_id	3cr3D00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	510 — Phosphotransferase system, mannose-type IIA component

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Unit-cell length a length_a	74.133 Å
Unit-cell length b length_b	146.842 Å
Unit-cell length c length_c	58.483 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.100 Å
Low-resolution limit resolution_low	66.230 Å
R factor r_factor	0.2217
R_work r_work	0.2190
R_free r_free	0.2630

Structure of a transient complex between Dha-kinase subunits DhaM and DhaL from Lactococcus lactis

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

PTS-dependent dihydroxyacetone kinase, ADP-binding subunit dhaL

State in the Current Structure

Other States of the Same Protein in the Database

PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM

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

3cr3__assembly_3__model_1

3cr3__assembly_3__model_1 | I(q)

3cr3__assembly_3__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

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Structure of a transient complex between Dha-kinase subunits DhaM and DhaL from Lactococcus lactis

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

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

PTS-dependent dihydroxyacetone kinase, phosphotransferase subunit dhaM

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

3cr3__assembly_3__model_1

3cr3__assembly_3__model_1 | I(q)

3cr3__assembly_3__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

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 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)