SAXSdb — 2zf5

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

Glycerol kinase

Thermococcus kodakarensis

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 2	water × 2	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 6	water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLPK_PYRKO
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain O； PDBConstruct 1–497； UniProt 1–497 Author chain Y； PDBConstruct 1–497； UniProt 1–497

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	2zf5
Deposition date deposition_date	2007-12-20
Structure title title	Crystal Structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon
Keywords keywords	GLYCEROL KINASE, HYPERTHERMOPHILIC ARCHAEON, ATP-binding, Glycerol metabolism, Nucleotide-binding, 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.

2zf5__assembly_2__model_1

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

Download this curve (.dat)

2zf5__assembly_2__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

2zf5__assembly_2__model_1 | P(r) · Pending

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

Rg（Guinier）	52.14 Å
Rg (electron density)	51.56 Å
Total Rg	51.77 Å
Atom count	23526
Residues	2964
Excluded volume	419780 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`2zf5__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`2zf5__assembly_2__model_1`	hexameric （6）	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 (2)

Entity 1 Entity 1 polymer

Description description	Glycerol kinase
Molecular weight formula_weight	55969.5 kDa
EC 编号 ec_number	2.7.1.30
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	O,Y
Atom count atom_count	7975

MEKFVLSLDEGTTSARAIIFDRESNIHGIGQYEFPQHYPRPGWVEHNPEEIWDAQLRAIKDAIQSARIEPNQIAAIGVTNQRETTLVWDKDGKPLYNAIVWQCRRTAEMVEEIKREYGTMIKEKTGLVPDAYFSASKLKWLLDNVPGLREKAEKGEVMFGTVDTFLIYRLTGEHVTDYSNASRTMLFNIKKLDWDDELLELFDIPESVLPEVRESSEVYGYTKKELLGAEIPVSGDAGDQQAALFGQAAFEAGMVKATYGTGSFILVNTDKMVLYSDNLLTTIAWGLNGRVSYALEGSIFVTGAAVQWLRDGIKIIKHASETEELATKLESNEGVYFVPAFVGLGAPYWDQFARGIIIGITRGTGREHLARATLEAIAYLTRDVVDEMEKLVQIKELRVDGGATANDFLMQFQADILNRKVIRPVVKETTALGAAYLAGLAVDYWADTREIAELWKAERIFEPKMDEKTRERLYKGWKEAVKRAMGWAKVVDSAKSN

Source Source

Source organism organism	Thermococcus kodakarensis
NCBI taxonomy ID ncbi_taxonomy_id	69014
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	133

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6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d2zf5o1
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	d2zf5o2
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	d2zf5y1
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	d2zf5y2
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

CATH v4.4 (4 domains)

Domain ID domain_id	2zf5O01
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	2zf5O02
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	2zf5Y01
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	2zf5Y02
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	217.477 Å
Unit-cell length b length_b	217.477 Å
Unit-cell length c length_c	66.479 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	H 3
Space-group number int_tables_number	146
Crystal system crystal_system	—

Resolution resolution	2.400 Å
Low-resolution limit resolution_low	41.100 Å
R factor r_factor	0.1780
R_work r_work	0.1740
R_free r_free	0.2549

Crystal Structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon

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

2zf5__assembly_2__model_1

2zf5__assembly_2__model_1 | I(q)

2zf5__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)

Crystal Structure of highly thermostable glycerol kinase from a hyperthermophilic archaeon

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

2zf5__assembly_2__model_1

2zf5__assembly_2__model_1 | I(q)

2zf5__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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 water

6. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 domains)

7. Citations (1)