3bq7

SAM domain of Diacylglycerol Kinase delta1 (E35G)

Method: X-RAY DIFFRACTION

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

Diacylglycerol kinase delta

Homo sapiens

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	No other associated polymer	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	No other associated polymer	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 6	No other associated polymer	Consistent with protein count
4	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
5	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
6	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
7	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
8	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count
9	Protein monomer	Monomer	Protein 1	No other associated polymer	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DGKD_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 6–73； UniProt 1141–1208 Author chain B； PDBConstruct 6–73； UniProt 1141–1208 Author chain C； PDBConstruct 6–73； UniProt 1141–1208 Author chain D； PDBConstruct 6–73； UniProt 1141–1208 Author chain E； PDBConstruct 6–73； UniProt 1141–1208 Author chain F； PDBConstruct 6–73； UniProt 1141–1208

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	3bq7
Deposition date deposition_date	2007-12-19
Structure title title	SAM domain of Diacylglycerol Kinase delta1 (E35G)
Keywords keywords	;SAM domain, polymerization domain, Alternative splicing, Cytoplasm, Kinase, Membrane, Metal-binding, Phorbol-ester binding, Phosphoprotein, Transferase, Zinc, Zinc-finger ;; 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.

3bq7__assembly_2__model_1

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

Download this curve (.dat)

3bq7__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3bq7__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	27.86 Å
Rg (electron density)	26.70 Å
Total Rg	27.46 Å
Atom count	3345
Residues	411
Excluded volume	59763 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3bq7__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3bq7__assembly_2__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3bq7__assembly_3__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download
4	1	`3bq7__assembly_4__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
5	1	`3bq7__assembly_5__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
6	1	`3bq7__assembly_6__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
7	1	`3bq7__assembly_7__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
8	1	`3bq7__assembly_8__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
9	1	`3bq7__assembly_9__model_1`	monomeric （1）	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 (1)

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6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

Domain ID domain_id	d3bq7a1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d3bq7a2
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	d3bq7b_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d3bq7c1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d3bq7c2
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	d3bq7d_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d3bq7e1
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

Domain ID domain_id	d3bq7e2
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	d3bq7f_
Class class	a — All alpha proteins
Fold Fold fold	a.60 — SAM domain-like
Superfamily Superfamily superfamily	a.60.1 — SAM/Pointed domain
Family Family family	a.60.1.0 — automated matches

CATH v4.4 (6 domains)

Domain ID domain_id	3bq7A00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

Domain ID domain_id	3bq7B00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

Domain ID domain_id	3bq7C00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

Domain ID domain_id	3bq7D00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

Domain ID domain_id	3bq7E00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

Domain ID domain_id	3bq7F00
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	150 — DNA polymerase; domain 1
Homologous superfamily homologous superfamily	50 — Transcription Factor, Ets-1

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Unit-cell length a length_a	108.079 Å
Unit-cell length b length_b	108.079 Å
Unit-cell length c length_c	33.513 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	18

Space group space_group	P 32
Space-group number int_tables_number	145
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	54.040 Å
R factor r_factor	0.2540
R_work r_work	0.2500
R_free r_free	0.2900

Description description	Diacylglycerol kinase delta
Molecular weight formula_weight	9601.1 kDa
EC 编号 ec_number	2.7.1.107
Mutation mutation	E35G
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	3320

SAM domain of Diacylglycerol Kinase delta1 (E35G)

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

Diacylglycerol kinase delta

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

3bq7__assembly_2__model_1

3bq7__assembly_2__model_1 | I(q)

3bq7__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Source organism organism	Homo sapiens
Common name common_name	human
NCBI taxonomy ID ncbi_taxonomy_id	9606
Host organism host_organism	Escherichia coli

SAM domain of Diacylglycerol Kinase delta1 (E35G)

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

Diacylglycerol kinase delta

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

3bq7__assembly_2__model_1

3bq7__assembly_2__model_1 | I(q)

3bq7__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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

6. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (9 domains)

CATH v4.4 (6 domains)

7. Citations (1)