SAXSdb — 5d56

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

Diacylglycerol kinase

Escherichia coli K-12

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 3	(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE × 8 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 3	(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE × 3 ZINC ION × 1 CITRATE ANION × 1 ACETATE ION × 1 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	KDGL_ECOLI
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 10–130； UniProt 2–122 Author chain B； PDBConstruct 10–130； UniProt 2–122 Author chain C； PDBConstruct 10–130； UniProt 2–122 Author chain D； PDBConstruct 10–130； UniProt 2–122 Author chain E； PDBConstruct 10–130； UniProt 2–122 Author chain F； PDBConstruct 10–130； UniProt 2–122

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	5d56
Deposition date deposition_date	2015-08-10
Structure title title	In meso in situ serial X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K
Keywords keywords	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.

5d56__assembly_1__model_1

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

Download this curve (.dat)

5d56__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

5d56__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	20.99 Å
Rg (electron density)	19.68 Å
Total Rg	20.52 Å
Atom count	2485
Residues	303
Excluded volume	46221 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`5d56__assembly_1__model_1`	trimeric （3）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`5d56__assembly_2__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	Diacylglycerol kinase
Molecular weight formula_weight	14204.5 kDa
EC 编号 ec_number	2.7.1.107
Mutation mutation	A41C, C46A, I53V, I70L, M96L, V107D and C113A
Source method src_method	man
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	4717

GHHHHHHELANNTTGFTRIIKAAGYSWKGLRAAWINEAAFRQEGVAVLLCVVIAAWLDVDAVTRVLLISSVMLVMIVELLNSAIEAVVDRIGSEYHELSGRAKDLGSAAVLIAIIDAVITWAILLWSHFG

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 non-polymer

Description description	(2S)-2,3-DIHYDROXYPROPYL(7Z)-PENTADEC-7-ENOATE
Molecular weight formula_weight	314.5 kDa
Source method src_method	syn
Copy count entity_count	11

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	CITRATE ANION
Molecular weight formula_weight	189.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

Description description	ACETATE ION
Molecular weight formula_weight	59.0 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	13

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6. Fold Classification (SCOP + CATH) 11 domains

SCOP 2.08 (5 domains)

Domain ID domain_id	d5d56a_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.62 — Diacylglycerol kinase (DgkA)-like
Superfamily Superfamily superfamily	f.62.1 — Diacylglycerol kinase (DgkA)-like
Family Family family	f.62.1.1 — Diacylglycerol kinase (DgkA)-like

Domain ID domain_id	d5d56b_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.62 — Diacylglycerol kinase (DgkA)-like
Superfamily Superfamily superfamily	f.62.1 — Diacylglycerol kinase (DgkA)-like
Family Family family	f.62.1.1 — Diacylglycerol kinase (DgkA)-like

Domain ID domain_id	d5d56c_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.62 — Diacylglycerol kinase (DgkA)-like
Superfamily Superfamily superfamily	f.62.1 — Diacylglycerol kinase (DgkA)-like
Family Family family	f.62.1.1 — Diacylglycerol kinase (DgkA)-like

Domain ID domain_id	d5d56d_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.62 — Diacylglycerol kinase (DgkA)-like
Superfamily Superfamily superfamily	f.62.1 — Diacylglycerol kinase (DgkA)-like
Family Family family	f.62.1.1 — Diacylglycerol kinase (DgkA)-like

Domain ID domain_id	d5d56e_
Class class	f — Membrane and cell surface proteins and peptides
Fold Fold fold	f.62 — Diacylglycerol kinase (DgkA)-like
Superfamily Superfamily superfamily	f.62.1 — Diacylglycerol kinase (DgkA)-like
Family Family family	f.62.1.1 — Diacylglycerol kinase (DgkA)-like

CATH v4.4 (6 domains)

Domain ID domain_id	5d56A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3610 —

Domain ID domain_id	5d56B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3610 —

Domain ID domain_id	5d56C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3610 —

Domain ID domain_id	5d56D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3610 —

Domain ID domain_id	5d56E00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3610 —

Domain ID domain_id	5d56F00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	3610 —

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Unit-cell length a length_a	74.800 Å
Unit-cell length b length_b	93.040 Å
Unit-cell length c length_c	143.050 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	24

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	2.800 Å
Low-resolution limit resolution_low	46.520 Å
R factor r_factor	0.2452
R_work r_work	0.2432
R_free r_free	0.2831

In meso in situ serial X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K

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

Diacylglycerol kinase

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

5d56__assembly_1__model_1

5d56__assembly_1__model_1 | I(q)

5d56__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 non-polymer

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) 11 domains

SCOP 2.08 (5 domains)

CATH v4.4 (6 domains)

7. Citations (1)

In meso in situ serial X-ray crystallography structure of diacylglycerol kinase, DgkA, at 100 K

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

Diacylglycerol kinase

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

5d56__assembly_1__model_1

5d56__assembly_1__model_1 | I(q)

5d56__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 non-polymer

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) 11 domains

SCOP 2.08 (5 domains)

CATH v4.4 (6 domains)

7. Citations (1)