SAXSdb — 6jna

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

Glutamate dehydrogenase

Thermococcus profundus

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein monomer	Monomer	Protein 1	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	DHE3_THEPR
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–419； UniProt 1–419

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	6jna
Deposition date deposition_date	2019-03-14
Structure title title	Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus
Keywords keywords	enzyme, multi-domain protein, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	ELECTRON MICROSCOPY

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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.

6jna__assembly_1__model_1

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

Download this curve (.dat)

6jna__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

6jna__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	23.59 Å
Rg (electron density)	22.44 Å
Total Rg	23.41 Å
Atom count	3294
Residues	419
Excluded volume	58965 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`6jna__assembly_1__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 (2)

Entity 1 Entity 1 polymer

Description description	Glutamate dehydrogenase
Molecular weight formula_weight	46758.5 kDa
EC 编号 ec_number	1.4.1.3
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	3294

MVEIDPFEMAVKQLERAAQYMDISEEALEWLKKPMRIVEVSVPIEMDDGSVKVFTGFRVQHNWARGPTKGGIRWHPAETLSTVKALATWMTWKVAVVDLPYGGGKGGIIVNPKELSEREQERLARAYIRAVYDVIGPWTDIPAPDVYTNPKIMGWMMDEYETIMRRKGPAFGVITGKPLSIGGSLGRGTATAQGAIFTIREAAKALGIDLKGKKIAVQGYGNAGYYTAKLAKEQLGMTVVAVSDSRGGIYNPDGLDPDEVLKWKREHGSVKDFPGATNITNEELLELEVDVLAPAAIEEVITEKNADNIKAKIVAEVANGPVTPEADDILREKGILQIPDFLCNAGGVTVSYFEWVQNINGYYWTEEEVREKLDKKMTKAFWEVYNTHKDKNIHMRDAAYVVAVSRVYQAMKDRGWVKK

Source Source

Source organism organism	Thermococcus profundus
NCBI taxonomy ID ncbi_taxonomy_id	49899
Host organism host_organism	Escherichia coli

Entity 2 Entity 2 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

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6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	6jnaA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	10860 — Leucine Dehydrogenase, chain A, domain 1

Domain ID domain_id	6jnaA02
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	50 — Rossmann fold
Homologous superfamily homologous superfamily	720 — NAD(P)-binding Rossmann-like Domain

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Unit-cell length a length_a	1.000 Å
Unit-cell length b length_b	1.000 Å
Unit-cell length c length_c	1.000 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	1

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

Resolution resolution	3.80 Å
Resolution测定Method resolution_method	—
颗粒数 num_particles	109568

Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus

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

Glutamate 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

6jna__assembly_1__model_1

6jna__assembly_1__model_1 | I(q)

6jna__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)

Cryo-EM structure of glutamate dehydrogenase from Thermococcus profundus

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

Glutamate 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

6jna__assembly_1__model_1

6jna__assembly_1__model_1 | I(q)

6jna__assembly_1__model_1 | P(r) · Pending

4. Crystallography and Experiment 4. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

冷冻电镜 EM 3D

5. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Source Source

Entity 2 Entity 2 non-polymer

6. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

7. Citations (1)