6k79

Glycerol kinase form Thermococcus kodakarensis, complex structure with substrate.

Method: X-RAY DIFFRACTION

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

Glycerol kinase

Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)

State in the Current Structure

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

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	GLPK_THEKO
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain B； PDBConstruct 1–497； UniProt 1–497 Author chain A； PDBConstruct 1–497； UniProt 1–497 Author chain C； PDBConstruct 1–497； UniProt 1–497 Author chain D； 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	6k79
Deposition date deposition_date	2019-06-06
Structure title title	Glycerol kinase form Thermococcus kodakarensis, complex structure with substrate.
Keywords keywords	Glycerol, Kinase, ATP, Archaea, 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.

6k79__assembly_1__model_1

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

Download this curve (.dat)

6k79__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6k79__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	38.09 Å
Rg (electron density)	38.22 Å
Total Rg	38.39 Å
Atom count	7821
Residues	980
Excluded volume	139610 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6k79__assembly_1__model_1`	dimeric （2）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`6k79__assembly_2__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	55984.4 kDa
EC 编号 ec_number	2.7.1.30
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B
Atom count atom_count	16106

MEKFVLSLDEGTTSARAIIFDRESNIHGIGQYEFPQHYPRPGWVEHNPEEIWDAQLRAIKDAIQSARIEPNQIAAIGVTNQRETTLVWDKDGKPLYNAIVWQCRRTAEMVEEIKREYGTMIKEKTGLVPDAYFSASKLKWLLDNLPGLREKAEKGEVMFGTVDTFLIYRLTGEHVTDYSNASRTMLFNIKKLDWDDELLELFDIPESVLPEVRESSEVYGYTKKELLGAEIPVSGDAGDQQAALFGEAAFEAGMVKATYGTGSFILVNTDEMVLYSDNLLTTIAWGLNGRVSYALEGSIFVTGAAVQWLRDGIKIIKHASETEELATKLESNEGVYFVPAFVGLGAPYWDQFARGIIIGITRGTGREHLARATLEAIAYLTRDVVDEMEKLVQIKELRVDGGATANDFLMQFQADILNRKVIRPVVKETTALGAAYLAGLAVDYWADTREIAELWKAERIFEPKMDEKTRERLYKGWKEAVKRAMGWAKVVDSAKSN

Source Source

Source organism organism	Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
NCBI taxonomy ID ncbi_taxonomy_id	69014
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Glycerol kinase
Molecular weight formula_weight	55969.4 kDa
EC 编号 ec_number	2.7.1.30
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

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

MEKFVLSLDEGTTSARAIIFDRESNIHGIGQYEFPQHYPRPGWVEHNPEEIWDAQLRAIKDAIQSARIEPNQIAAIGVTNQRETTLVWDKDGKPLYNAIVWQCRRTAEMVEEIKREYGTMIKEKTGLVPDAYFSASKLKWLLDNVPGLREKAEKGEVMFGTVDTFLIYRLTGEHVTDYSNASRTMLFNIKKLDWDDELLELFDIPESVLPEVRESSEVYGYTKKELLGAEIPVSGDAGDQQAALFGQAAFEAGMVKATYGTGSFILVNTDEMVLYSDNLLTTIAWGLNGRVSYALEGSIFVTGAAVQWLRDGIKIIKHASETEELATKLESNEGVYFVPAFVGLGAPYWDQFARGIIIGITRGTGREHLARATLEAIAYLTRDVVDEMEKLVQIKELRVDGGATANDFLMQFQADILNRKVIRPVVKETTALGAAYLAGLAVDYWADTREIAELWKAERIFEPKMDEKTRERLYKGWKEAVKRAMGWAKVVDSAKSN

Source Source

Source organism organism	Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 / KOD1)
NCBI taxonomy ID ncbi_taxonomy_id	69014
Host organism host_organism	Escherichia coli

Entity 3 Entity 3 non-polymer

Description description	TRIETHYLENE GLYCOL
Molecular weight formula_weight	150.2 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 non-polymer

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

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	457

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6. Fold Classification (SCOP + CATH) 14 domains

SCOP 2.08 (8 domains)

Domain ID domain_id	d6k79a1
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	d6k79a2
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	d6k79b1
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	d6k79b2
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	d6k79c1
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	d6k79c2
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	d6k79d1
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	d6k79d2
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 (6 domains)

Domain ID domain_id	6k79A01
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	6k79A02
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	6k79B01
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	6k79C01
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	6k79C02
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	6k79D01
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	67.041 Å
Unit-cell length b length_b	72.128 Å
Unit-cell length c length_c	115.994 Å
Unit-cell angle α angle_alpha	103.43 °
Unit-cell angle β angle_beta	94.96 °
Unit-cell angle γ angle_gamma	99.48 °
Molecules per unit cell Z z_pdb	3

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

Resolution resolution	2.190 Å
Low-resolution limit resolution_low	46.200 Å
R factor r_factor	0.1872
R_work r_work	0.1846
R_free r_free	0.2378

Glycerol kinase form Thermococcus kodakarensis, complex structure with substrate.

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

6k79__assembly_1__model_1

6k79__assembly_1__model_1 | I(q)

6k79__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 (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) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)

Glycerol kinase form Thermococcus kodakarensis, complex structure with substrate.

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

6k79__assembly_1__model_1

6k79__assembly_1__model_1 | I(q)

6k79__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 (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) 14 domains

SCOP 2.08 (8 domains)

CATH v4.4 (6 domains)

7. Citations (1)