3g25

1.9 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with Glycerol.

Method: X-RAY DIFFRACTION

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

Glycerol kinase

Staphylococcus aureus subsp. aureus COL

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 2 SODIUM ION × 5 PHOSPHATE ION × 9 water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 4	GLYCEROL × 4 SODIUM ION × 7 PHOSPHATE ION × 13 water × 4	Consistent with protein count
3	Protein homooligomer	Homooligomer	Protein 2	GLYCEROL × 2 SODIUM ION × 2 PHOSPHATE ION × 4 water × 2	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLPK_STAAC
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 4–501； UniProt 1–498 Author chain B； PDBConstruct 4–501； UniProt 1–498 Author chain C； PDBConstruct 4–501； UniProt 1–498 Author chain D； PDBConstruct 4–501； UniProt 1–498

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	3g25
Deposition date deposition_date	2009-01-30
Structure title title	1.9 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with Glycerol.
Keywords keywords	;Glycerol kinase, Glycerol, idp00743, ATP-binding, Glycerol metabolism, Kinase, Nucleotide-binding, Transferase, Structural Genomics, Center for Structural Genomics of Infectious Diseases, CSGID ;; 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.

3g25__assembly_3__model_1

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

Download this curve (.dat)

3g25__assembly_3__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3g25__assembly_3__model_1 | P(r) · Pending

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

Rg（Guinier）	34.13 Å
Rg (electron density)	33.97 Å
Total Rg	34.35 Å
Atom count	7883
Residues	975
Excluded volume	139760 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3g25__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`3g25__assembly_2__model_1`	tetrameric （4）	Success	4.1.3-1-20251215 (887e7ef)	View Download
3	1	`3g25__assembly_3__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	Glycerol kinase
Molecular weight formula_weight	56471.4 kDa
EC 编号 ec_number	2.7.1.30
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	17856

SNAMEKYILSIDQGTTSSRAILFNQKGEIAGVAQREFKQYFPQSGWVEHDANEIWTSVLAVMTEVINENDVRADQIAGIGITNQRETTVVWDKHTGRPIYHAIVWQSRQTQSICSELKQQGYEQTFRDKTGLLLDPYFAGTKVKWILDNVEGAREKAENGDLLFGTIDTWLVWKLSGKAAHITDYSNASRTLMFNIHDLEWDDELLELLTVPKNMLPEVKASSEVYGKTIDYHFYGQEVPIAGVAGDQQAALFGQACFERGDVKNTYGTGGFMLMNTGDKAVKSESGLLTTIAYGIDGKVNYALEGSIFVSGSAIQWLRDGLRMINSAPQSESYATRVDSTEGVYVVPAFVGLGTPYWDSEARGAIFGLTRGTEKEHFIRATLESLCYQTRDVMEAMSKDSGIDVQSLRVDGGAVKNNFIMQFQADIVNTSVERPEIQETTALGAAFLAGLAVGFWESKDDIAKNWKLEEKFDPKMDEGEREKLYRGWKKAVEATQVFKTE

Source Source

Source organism organism	Staphylococcus aureus subsp. aureus COL
NCBI taxonomy ID ncbi_taxonomy_id	93062
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	GLYCEROL
Molecular weight formula_weight	92.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 3 Entity 3 non-polymer

Description description	SODIUM ION
Molecular weight formula_weight	23.0 kDa
Source method src_method	syn
Copy count entity_count	7

Entity 4 Entity 4 non-polymer

Description description	PHOSPHATE ION
Molecular weight formula_weight	95.0 kDa
Source method src_method	syn
Copy count entity_count	13

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	1174

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6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (11 domains)

Domain ID domain_id	d3g25a1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d3g25a2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d3g25a3
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	d3g25b1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d3g25b2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d3g25b3
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	d3g25c1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d3g25c2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d3g25d1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d3g25d2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.55 — Ribonuclease H-like motif
Superfamily Superfamily superfamily	c.55.1 — Actin-like ATPase domain
Family Family family	c.55.1.0 — automated matches

Domain ID domain_id	d3g25d3
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 (8 domains)

Domain ID domain_id	3g25A01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3g25A02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3g25B01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3g25B02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3g25C01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3g25C02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3g25D01
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

Domain ID domain_id	3g25D02
Class class	3 — Alpha Beta
Architecture architecture	30 — 2-Layer Sandwich
Topology topology	420 — Nucleotidyltransferase; domain 5
Homologous superfamily homologous superfamily	40 — ATPase, nucleotide binding domain

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Unit-cell length a length_a	63.750 Å
Unit-cell length b length_b	193.742 Å
Unit-cell length c length_c	91.669 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	103.60 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	—

Resolution resolution	1.900 Å
Low-resolution limit resolution_low	44.810 Å
R factor r_factor	0.1953
R_work r_work	0.1927
R_free r_free	0.2456

1.9 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with Glycerol.

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

Glycerol 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

3g25__assembly_3__model_1

3g25__assembly_3__model_1 | I(q)

3g25__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (11 domains)

CATH v4.4 (8 domains)

7. Citations (1)

1.9 Angstrom Crystal Structure of Glycerol Kinase (glpK) from Staphylococcus aureus in Complex with Glycerol.

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

Glycerol 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

3g25__assembly_3__model_1

3g25__assembly_3__model_1 | I(q)

3g25__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 19 domains

SCOP 2.08 (11 domains)

CATH v4.4 (8 domains)

7. Citations (1)