1hrd

GLUTAMATE DEHYDROGENASE

Method: X-RAY DIFFRACTION D_max: 105.2 Å Quality: EXCELLENT

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

GLUTAMATE DEHYDROGENASE

OrganismNot specified

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Protein homooligomer Homooligomer Protein × 6 PDB declaration: hexameric（6） Consistent with protein copy count	Chain A； UniProt 1–449 Chain B； UniProt 1–449 Chain C； UniProt 1–449	Not recorded	No other associated polymer	X-RAY DIFFRACTION mmCIF provides none of the parsed experimental conditions	Resolution 1.96 Å

Other States of the Same Protein in the Database

Each row is a biological assembly of the same UniProt protein in another PDB entry. The “Difference from current entry” column identifies evidence-level differences; no tag means the currently parsed fields agree.

Other PDB	Difference from Current Entry 1HRD	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1AUP GLUTAMATE DEHYDROGENASE Deposited 1997-09-01	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–449（449 aa）	Mutation：K89L, S380V	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.50 Å
1BGV GLUTAMATE DEHYDROGENASE Deposited 1998-06-01	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–449（449 aa）	Not recorded	GLU GLUTAMIC ACID × 6	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 1.90 Å
1K89 K89L MUTANT OF GLUTAMATE DEHYDROGENASE Deposited 1998-06-05	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–449（449 aa）	Mutation：K89L	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 7；pH 7.0	Resolution 2.05 Å

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DHE2_CLOSY
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–449； UniProt 1–449 Author chain B； PDBConstruct 1–449； UniProt 1–449 Author chain C； PDBConstruct 1–449； UniProt 1–449

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.

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

Download Download SAXS (.dat) P(r) (.pr.out) CIF

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	1hrd
Deposition date deposition_date	1996-04-03
Structure title title	GLUTAMATE DEHYDROGENASE
Keywords keywords	OXIDOREDUCTASE, NAD; OXIDOREDUCTASE
Experimental Method method	X-RAY DIFFRACTION

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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier	35.06 Å
Radius of gyration Rg (electron density) rg_electron	34.36 Å
Forward intensity I(0) i0	331173000.00
Molecular weight molecular_weight	147460.0 kDa
Excluded volume excluded_volume	184490 Å³
Envelope volume envelope_volume	227820 Å³
Hydration-shell volume shell_volume	53376 Å³
Envelope diameter envelope_diameter	107.2 Å
Shell Rg shell_rg	42.49 Å
Envelope Rg envelope_rg	34.11 Å
Shape Rg shape_rg	34.38 Å
Total Rg total_rg	34.87 Å
Total atoms total_atoms	10380
Residues n_residues	1347
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	105.2 Å
Rg (real space) rg_real	34.87 Å
Rg uncertainty (real space) rg_real_error	0.53 Å
I(0) (real space) i0_real	3.3120e+08
I(0) uncertainty (real space) i0_real_error	5.3230e+06
Rg (reciprocal space) rg_reciprocal	34.99 Å
I(0) (reciprocal space) i0_reciprocal	331200000.0000
Solution quality estimate total_estimate	0.9022
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	44.4 Å
Skewness Skewness skewness	0.104
Kurtosis Kurtosis kurtosis	-0.597
Angular range angular_range	— – 0.2250 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	37660000.0000
Real-space data points n_real_points	46
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.968; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.985; Smooth: 0.836

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

Domain ID domain_id	d1hrda1
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	d1hrda2
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	d1hrdb1
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	d1hrdb2
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	d1hrdc1
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	d1hrdc2
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

CATH v4.4 (9 domains)

Domain ID domain_id	1hrdA01
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	1hrdA02
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	1hrdA03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Glutamate Dehydrogenase, chain A, domain 3

Domain ID domain_id	1hrdB01
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	1hrdB02
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	1hrdB03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Glutamate Dehydrogenase, chain A, domain 3

Domain ID domain_id	1hrdC01
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	1hrdC02
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	1hrdC03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	285 — Glutamate Dehydrogenase; Chain A, domain 3
Homologous superfamily homologous superfamily	10 — Glutamate Dehydrogenase, chain A, domain 3

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8. Citations (5)

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Unit-cell length a length_a	147.100 Å
Unit-cell length b length_b	151.300 Å
Unit-cell length c length_c	94.600 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	132.75 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	1.960 Å
Low-resolution limit resolution_low	37.800 Å
R factor r_factor	—
R_work r_work	0.1720
R_free r_free	—

Description description	GLUTAMATE DEHYDROGENASE
Molecular weight formula_weight	49215.6 kDa
EC 编号 ec_number	1.4.1.2
Source method src_method	nat
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	10901

GLUTAMATE DEHYDROGENASE

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

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 15 domains

SCOP 2.08 (6 domains)

CATH v4.4 (9 domains)

8. Citations (5)

9. Files and Curves (10)

Files (7)

Curves (3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	521

fit	/app/data/saxs_computation/hr/1hrd/1hrd.fit
pddf	/app/data/pr_computation/hr/1hrd/1hrd.pr.out
profile	/app/data/saxs_computation/hr/1hrd/1hrd.dat