1nr1

Crystal structure of the R463A mutant of human Glutamate dehydrogenase

Method: X-RAY DIFFRACTION D_max: 141.5 Å Quality: GOOD

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

Glutamate dehydrogenase 1

Homo sapiens

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 63–558 Chain B； UniProt 63–558 Chain C； UniProt 63–558 Chain D； UniProt 63–558 Chain E； UniProt 63–558 Chain F； UniProt 63–558	Mutation：R463A	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 6.8；298 K；sodium phosphate, PEG 8000, BOG, sodium chloride, MPD, sodium azide, pH 6.8, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 3.30 Å R-free 0.284

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 1NR1	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1L1F Structure of human glutamate dehydrogenase-apo form Deposited 2002-02-15	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 54–558（505 aa） Chain B 54–558（505 aa） Chain C 54–558（505 aa） Chain D 54–558（505 aa） Chain E 54–558（505 aa） Chain F 54–558（505 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 7；298 K；PEG 8000, NaCl, sodium phosphate, sodium azide, octyl-b-glucopyranoside, methyl pentanediol, pH 7, VAPOR DIFFUSION, SITTING DROP, temperature 298K	Resolution 2.70 Å R-free 0.302
6DQG Human glutamate dehydrogenase, H454Y mutant Deposited 2018-06-10	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 63–558（496 aa） Fragment：UNP residues 63-558 Chain B 63–558（496 aa） Fragment：UNP residues 63-558 Chain C 63–558（496 aa） Fragment：UNP residues 63-558 Chain D 63–558（496 aa） Fragment：UNP residues 63-558 Chain E 63–558（496 aa） Fragment：UNP residues 63-558 Chain F 63–558（496 aa） Fragment：UNP residues 63-558	Mutation：H454Y Mutation：H454Y Mutation：H454Y Mutation：H454Y Mutation：H454Y Mutation：H454Y	PO4 PHOSPHATE ION × 15	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.8；295 K；Reservoir: 10% w/v PEG8000, 0.1 M sodium chloride, 1.3% w/v octyl-b-glucopyranoside, 7.5% v/v MPD, 0.1 M sodium phosphate, pH 6.8, 1 mM sodium azide	Resolution 2.70 Å R-free 0.279
7UZM Glutamate dehydrogenase 1 from human liver Deposited 2022-05-09	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–558（558 aa） Chain B 1–558（558 aa） Chain C 1–558（558 aa） Chain D 1–558（558 aa） Chain E 1–558（558 aa） Chain F 1–558（558 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.24 Å
8KGY Human glutamate dehydrogenase I Deposited 2023-08-20	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–558（558 aa） Chain B 1–558（558 aa） Chain C 1–558（558 aa） Chain D 1–558（558 aa） Chain E 1–558（558 aa） Chain F 1–558（558 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；20 mM HEPES pH 7.4, 200 mM NaCl, 2 mM MgCl2 and 0.5 mM TCEP cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.59 Å
8SK8 human liver mitochondrial Glutamate dehydrogenase 1 Deposited 2023-04-18	Different construct Different mutation/modification Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 1–558（558 aa） Chain B 1–558（558 aa） Chain C 1–558（558 aa） Chain D 1–558（558 aa） Chain E 1–558（558 aa） Chain F 1–558（558 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 2.31 Å
8W4J Cryo-EM structure of the KLHL22 E3 ligase bound to human glutamate dehydrogenase I Deposited 2023-08-24	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain A 1–558（558 aa） Chain B 1–558（558 aa） Chain C 1–558（558 aa） Chain D 1–558（558 aa） Chain E 1–558（558 aa） Chain F 1–558（558 aa）	Not recorded	No recorded non-water small molecule	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.06 Å

6 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	DHE3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–496； UniProt 63–558 Author chain B； PDBConstruct 1–496； UniProt 63–558 Author chain C； PDBConstruct 1–496； UniProt 63–558 Author chain D； PDBConstruct 1–496； UniProt 63–558 Author chain E； PDBConstruct 1–496； UniProt 63–558 Author chain F； PDBConstruct 1–496； UniProt 63–558

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	1nr1
Deposition date deposition_date	2003-01-23
Structure title title	Crystal structure of the R463A mutant of human Glutamate dehydrogenase
Keywords keywords	glutamate dehydrogenase, hexamer, regulation, OXIDOREDUCTASE; 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	43.87 Å
Radius of gyration Rg (electron density) rg_electron	43.49 Å
Forward intensity I(0) i0	1589910000.00
Molecular weight molecular_weight	329700.0 kDa
Excluded volume excluded_volume	412290 Å³
Envelope volume envelope_volume	528090 Å³
Hydration-shell volume shell_volume	95723 Å³
Envelope diameter envelope_diameter	149.9 Å
Shell Rg shell_rg	51.67 Å
Envelope Rg envelope_rg	43.44 Å
Shape Rg shape_rg	43.47 Å
Total Rg total_rg	43.87 Å
Total atoms total_atoms	23208
Residues n_residues	2976
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	141.5 Å
Rg (real space) rg_real	43.67 Å
Rg uncertainty (real space) rg_real_error	1.01 Å
I(0) (real space) i0_real	1.5900e+09
I(0) uncertainty (real space) i0_real_error	2.6610e+07
Rg (reciprocal space) rg_reciprocal	43.87 Å
I(0) (reciprocal space) i0_reciprocal	1590000000.0000
Solution quality estimate total_estimate	0.8787
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	55.0 Å
Skewness Skewness skewness	0.237
Kurtosis Kurtosis kurtosis	-0.344
Angular range angular_range	— – 0.1800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	334600000.0000
Real-space data points n_real_points	37
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.842; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.915

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

Domain ID domain_id	d1nr1a1
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	d1nr1a2
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	d1nr1b1
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	d1nr1b2
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	d1nr1c1
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	d1nr1c2
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	d1nr1d1
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	d1nr1d2
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	d1nr1e1
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	d1nr1e2
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	d1nr1f1
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	d1nr1f2
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 (18 domains)

Domain ID domain_id	1nr1A01
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	1nr1A02
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	1nr1A03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	1nr1B01
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	1nr1B02
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	1nr1B03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	1nr1C01
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	1nr1C02
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	1nr1C03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	1nr1D01
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	1nr1D02
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	1nr1D03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	1nr1E01
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	1nr1E02
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	1nr1E03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	140 —

Domain ID domain_id	1nr1F01
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	1nr1F02
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	1nr1F03
Class class	1 — Mainly Alpha
Architecture architecture	10 — Orthogonal Bundle
Topology topology	287 — Helix Hairpins
Homologous superfamily homologous superfamily	140 —

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8. Citations (1)

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Unit-cell length a length_a	96.920 Å
Unit-cell length b length_b	98.640 Å
Unit-cell length c length_c	124.260 Å
Unit-cell angle α angle_alpha	86.48 °
Unit-cell angle β angle_beta	69.69 °
Unit-cell angle γ angle_gamma	60.87 °
Molecules per unit cell Z z_pdb	6

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

Resolution resolution	3.300 Å
Low-resolution limit resolution_low	19.990 Å
R factor r_factor	0.2220
R_work r_work	0.2220
R_free r_free	0.2840

Description description	Glutamate dehydrogenase 1
Molecular weight formula_weight	55025.5 kDa
EC 编号 ec_number	1.4.1.3
Mutation mutation	R463A
Source method src_method	man
Copy count entity_count	6

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D,E,F
Atom count atom_count	23208

Crystal structure of the R463A mutant of human Glutamate dehydrogenase

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

Glutamate dehydrogenase 1

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

CATH v4.4 (18 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

fit	/app/data/saxs_computation/nr/1nr1/1nr1.fit
pddf	/app/data/pr_computation/nr/1nr1/1nr1.pr.out
profile	/app/data/saxs_computation/nr/1nr1/1nr1.dat