SAXSdb — 1kq3

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

glycerol dehydrogenase

Thermotoga maritima

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	ZINC ION × 1 CHLORIDE ION × 1 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1 water × 1	Consistent with protein count
2	Protein homooligomer	Homooligomer	Protein 8	ZINC ION × 8 CHLORIDE ION × 8 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 8 water × 8	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q9WYQ4_THEMA
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 13–376； UniProt 1–364

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	1kq3
Deposition date deposition_date	2002-01-03
Structure title title	CRYSTAL STRUCTURE OF A GLYCEROL DEHYDROGENASE (TM0423) FROM THERMOTOGA MARITIMA AT 1.5 A RESOLUTION
Keywords keywords	;GLYCEROL DEHYDROGENASE, STRUCTURAL GENOMICS, JOINT CENTER FOR STRUCTURAL GENOMICS, JCSG, PROTEIN STRUCTURE INITIATIVE, PSI, OXIDOREDUCTASE ;; OXIDOREDUCTASE
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.

1kq3__assembly_1__model_1

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

Download this curve (.dat)

1kq3__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

1kq3__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	21.67 Å
Rg (electron density)	20.64 Å
Total Rg	21.53 Å
Atom count	2802
Residues	364
Excluded volume	50323 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`1kq3__assembly_1__model_1`	monomeric （1）	Success	4.1.3-1-20251215 (887e7ef)	View Download
2	1	`1kq3__assembly_2__model_1`	octameric （8）	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 dehydrogenase
Molecular weight formula_weight	41198.1 kDa
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	3029

MGSDKIHHHHHHMITTTIFPGRYVQGAGAINILEEELSRFGERAFVVIDDFVDKNVLGENFFSSFTKVRVNKQIFGGECSDEEIERLSGLVEEETDVVVGIGGGKTLDTAKAVAYKLKKPVVIVPTIASTDAPCSALSVIYTPNGEFKRYLFLPRNPDVVLVDTEIVAKAPARFLVAGMGDALATWFEAESCKQKYAPNMTGRLGSMTAYALARLCYETLLEYGVLAKRSVEEKSVTPALEKIVEANTLLSGLGFESGGLAAAHAIHNGLTVLENTHKYLHGEKVAIGVLASLFLTDKPRKMIEEVYSFCEEVGLPTTLAEIGLDGVSDEDLMKVAEKACDKNETIHNEPQPVTSKDVFFALKAADRYGRMRKNLT

Source Source

Source organism organism	Thermotoga maritima
NCBI taxonomy ID ncbi_taxonomy_id	2336
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	CHLORIDE ION
Molecular weight formula_weight	35.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	227

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6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1kq3a1
Class class	e — Multi-domain proteins (alpha and beta)
Fold Fold fold	e.22 — Dehydroquinate synthase-like
Superfamily Superfamily superfamily	e.22.1 — Dehydroquinate synthase-like
Family Family family	e.22.1.2 — Iron-containing alcohol dehydrogenase

Domain ID domain_id	d1kq3a2
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 (2 domains)

Domain ID domain_id	1kq3A01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	1970 —

Domain ID domain_id	1kq3A02
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	1090 — Dehydroquinate synthase-like, alpha domain
Homologous superfamily homologous superfamily	10 — Dehydroquinate synthase-like - alpha domain

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Unit-cell length a length_a	105.730 Å
Unit-cell length b length_b	105.730 Å
Unit-cell length c length_c	135.790 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	16

Space group space_group	I 4 2 2
Space-group number int_tables_number	97
Crystal system crystal_system	—

Resolution resolution	1.500 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.1730
R_work r_work	0.1730
R_free r_free	0.1890

CRYSTAL STRUCTURE OF A GLYCEROL DEHYDROGENASE (TM0423) FROM THERMOTOGA MARITIMA AT 1.5 A RESOLUTION

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

glycerol dehydrogenase

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

1kq3__assembly_1__model_1

1kq3__assembly_1__model_1 | I(q)

1kq3__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)

CRYSTAL STRUCTURE OF A GLYCEROL DEHYDROGENASE (TM0423) FROM THERMOTOGA MARITIMA AT 1.5 A RESOLUTION

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

glycerol dehydrogenase

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

1kq3__assembly_1__model_1

1kq3__assembly_1__model_1 | I(q)

1kq3__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 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

6. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

CATH v4.4 (2 domains)

7. Citations (1)