3etg

Glutamate dehydrogenase complexed with GW5074

Method: X-RAY DIFFRACTION

▼

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

Glutamate dehydrogenase

OrganismNot specified

State in the Current Structure

Assembly	Physical composition	Protein state	Molecular copy count	Associated components	Data consistency
1	Protein homooligomer	Homooligomer	Protein 6	GLUTAMIC ACID × 6 NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE × 6 GUANOSINE-5'-TRIPHOSPHATE × 6 (3E)-3-[(3,5-dibromo-4-hydroxyphenyl)methylidene]-5-iodo-1,3-dihydro-2H-indol-2-one × 6 water × 6	Consistent with protein count

Other States of the Same Protein in the Database

View Construct and Data Evidence

UniProt name	Q3SYY0_BOVIN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–501； UniProt 61–561 Author chain B； PDBConstruct 1–501； UniProt 61–561 Author chain C； PDBConstruct 1–501； UniProt 61–561 Author chain D； PDBConstruct 1–501； UniProt 61–561 Author chain E； PDBConstruct 1–501； UniProt 61–561 Author chain F； PDBConstruct 1–501； UniProt 61–561

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	3etg
Deposition date deposition_date	2008-10-07
Structure title title	Glutamate dehydrogenase complexed with GW5074
Keywords keywords	glutamate dehydrogenase, GW5074, inhibition, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

▼

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.

3etg__assembly_1__model_1

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

Download this curve (.dat)

3etg__assembly_1__model_1 | I(q)

100 plotted points; both axes use logarithmic scales.

3etg__assembly_1__model_1 | P(r) · Pending

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

Rg（Guinier）	43.18 Å
Rg (electron density)	42.80 Å
Total Rg	43.07 Å
Atom count	24150
Residues	3006
Excluded volume	426740 Å³
Maximum q	0.500 Å⁻¹

Assembly	Model	Structure unit	Oligomeric description	Status	CRYSOL	Actions
1	1	`3etg__assembly_1__model_1`	hexameric （6）	Success	4.1.3-1-20251215 (887e7ef)	View Download

▶

4. Crystallography and Experiment 4. Crystallography & Experiment

▶

5. Entities and Polymers Entities & Polymers (6)

Entity 1 Entity 1 polymer

Description description	Glutamate dehydrogenase
Molecular weight formula_weight	55715.2 kDa
Source method src_method	nat
Copy count entity_count	6

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	24305

ADREDDPNFFKMVEGFFDRGASIVEDKLVEDLKTRETEEQKRNRVRGILRIIKPCNHVLSLSFPIRRDDGSWEVIEGYRAQHSQHRTPCKGGIRYSTDVSVDEVKALASLMTYKCAVVDVPFGGAKAGVKINPKNYTDNELEKITRRFTMELAKKGFIGPGVDVPAPDMSTGEREMSWIADTYASTIGHYDINAHACVTGKPISQGGIHGRISATGRGVFHGIENFINEASYMSILGMTPGFGDKTFAVQGFGNVGLHSMRYLHRFGAKCVAVGESDGSIWNPDGIDPKELEDFKLQHGTILGFPKAKIYEGSILEVDCDILIPAASEKQLTKSNAPRVKAKIIAEGANGPTTPEADKIFLERNIMVIPDLYLNAGGVTVSYFEWLKNLNHVSYGRLTFKYERDSNYHLLMSVQESLERKFGKHGGTIPIVPTAEFQDRISGASEKDIVHSGLAYTMERSARQIMRTAMKYNLGLDLRTAAYVNAIEKVFRVYNEAGVTFT

Entity 2 Entity 2 non-polymer

Description description	GLUTAMIC ACID
Molecular weight formula_weight	147.1 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 3 Entity 3 non-polymer

Description description	NADPH DIHYDRO-NICOTINAMIDE-ADENINE-DINUCLEOTIDE PHOSPHATE
Molecular weight formula_weight	745.4 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 4 Entity 4 non-polymer

Description description	GUANOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	523.2 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 5 Entity 5 non-polymer

Description description	(3E)-3-[(3,5-dibromo-4-hydroxyphenyl)methylidene]-5-iodo-1,3-dihydro-2H-indol-2-one
Molecular weight formula_weight	520.9 kDa
Source method src_method	syn
Copy count entity_count	6

Entity 6 Entity 6 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	155

▼

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d3etga1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d3etga2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d3etgb1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d3etgb2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d3etgc1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d3etgc2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d3etgd1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d3etgd2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d3etge1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d3etge2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

Domain ID domain_id	d3etgf1
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamily	c.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family family	c.58.1.1 — Aminoacid dehydrogenases

Domain ID domain_id	d3etgf2
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamily	c.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family family	c.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

CATH v4.4 (18 domains)

Domain ID domain_id	3etgA01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	3etgA02
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	3etgA03
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

Domain ID domain_id	3etgB01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	3etgB02
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	3etgB03
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

Domain ID domain_id	3etgC01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	3etgC02
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	3etgC03
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

Domain ID domain_id	3etgD01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	3etgD02
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	3etgD03
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

Domain ID domain_id	3etgE01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	3etgE02
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	3etgE03
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

Domain ID domain_id	3etgF01
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	3etgF02
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	3etgF03
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

▶

Unit-cell length a length_a	122.300 Å
Unit-cell length b length_b	102.200 Å
Unit-cell length c length_c	167.700 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.50 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

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

Resolution resolution	2.500 Å
Low-resolution limit resolution_low	50.000 Å
R factor r_factor	0.2440
R_work r_work	0.2440
R_free r_free	0.2580

Glutamate dehydrogenase complexed with GW5074

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

3etg__assembly_1__model_1

3etg__assembly_1__model_1 | I(q)

3etg__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

CATH v4.4 (18 domains)

7. Citations (1)

Glutamate dehydrogenase complexed with GW5074

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

3etg__assembly_1__model_1

3etg__assembly_1__model_1 | I(q)

3etg__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 (6)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 non-polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 water

6. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

CATH v4.4 (18 domains)

7. Citations (1)