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6dqg

Human glutamate dehydrogenase, H454Y mutant

Method: X-RAY DIFFRACTION Dmax: 140.9 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Glutamate dehydrogenase 1, mitochondrial

Homo sapiens

UniProt P00367

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 Fragment：UNP residues 63-558 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

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 6DQG 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 ligand/ion 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
1NR1 Crystal structure of the R463A mutant of human Glutamate dehydrogenase Deposited 2003-01-23 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）
Chain B 63–558（496 aa）
Chain C 63–558（496 aa）
Chain D 63–558（496 aa）
Chain E 63–558（496 aa）
Chain F 63–558（496 aa）
Mutation：R463A Mutation：R463A Mutation：R463A Mutation：R463A Mutation：R463A Mutation：R463A No recorded non-water small molecule 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
7UZM Glutamate dehydrogenase 1 from human liver Deposited 2022-05-09 Different construct Different mutation/modification Different ligand/ion 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 ligand/ion 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 ligand/ion 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 ligand/ion 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

SAXS profile for 6dqg

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6dqg
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6dqg
Deposition date deposition_date2018-06-10
Structure title titleHuman glutamate dehydrogenase, H454Y mutant
Keywords keywordsGlutamate, dehydrogenase, insulin, hyperinsulinism, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier43.74 Å
Radius of gyration Rg (electron density) rg_electron43.37 Å
Forward intensity I(0) i01633080000.00
Molecular weight molecular_weight331800.0 kDa
Excluded volume excluded_volume413900 ų
Envelope volume envelope_volume529560 ų
Hydration-shell volume shell_volume96004 ų
Envelope diameter envelope_diameter150.0 Å
Shell Rg shell_rg51.70 Å
Envelope Rg envelope_rg43.38 Å
Shape Rg shape_rg43.35 Å
Total Rg total_rg43.75 Å
Total atoms total_atoms23331
Residues n_residues2976
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax140.9 Å
Rg (real space) rg_real43.55 Å
Rg uncertainty (real space) rg_real_error0.81 Å
I(0) (real space) i0_real1.6330e+09
I(0) uncertainty (real space) i0_real_error2.7060e+07
Rg (reciprocal space) rg_reciprocal43.74 Å
I(0) (reciprocal space) i0_reciprocal1633000000.0000
Solution quality estimate total_estimate0.8787
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary54.8 Å
Skewness Skewness skewness0.238
Kurtosis Kurtosis kurtosis-0.350
Angular range angular_range— – 0.1800 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha385700000.0000
Real-space data points n_real_points37
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.848; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.977; Smooth: 0.896
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (3)

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7. Fold Classification (SCOP + CATH) 30 domains

SCOP 2.08 (12 domains)

Domain ID domain_idd6dqga1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family familyc.58.1.1 — Aminoacid dehydrogenases
Domain ID domain_idd6dqga2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
Domain ID domain_idd6dqgb1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family familyc.58.1.1 — Aminoacid dehydrogenases
Domain ID domain_idd6dqgb2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
Domain ID domain_idd6dqgc1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family familyc.58.1.1 — Aminoacid dehydrogenases
Domain ID domain_idd6dqgc2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
Domain ID domain_idd6dqgd1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family familyc.58.1.1 — Aminoacid dehydrogenases
Domain ID domain_idd6dqgd2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
Domain ID domain_idd6dqge1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family familyc.58.1.1 — Aminoacid dehydrogenases
Domain ID domain_idd6dqge2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain
Domain ID domain_idd6dqgf1
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.58 — Aminoacid dehydrogenase-like, N-terminal domain
Superfamily Superfamily superfamilyc.58.1 — Aminoacid dehydrogenase-like, N-terminal domain
Family Family familyc.58.1.1 — Aminoacid dehydrogenases
Domain ID domain_idd6dqgf2
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.2 — NAD(P)-binding Rossmann-fold domains
Superfamily Superfamily superfamilyc.2.1 — NAD(P)-binding Rossmann-fold domains
Family Family familyc.2.1.7 — Aminoacid dehydrogenase-like, C-terminal domain

CATH v4.4 (18 domains)

Domain ID domain_id6dqgA01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily140 —
Domain ID domain_id6dqgA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
Domain ID domain_id6dqgA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6dqgB01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily140 —
Domain ID domain_id6dqgB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
Domain ID domain_id6dqgB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6dqgC01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily140 —
Domain ID domain_id6dqgC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
Domain ID domain_id6dqgC03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6dqgD01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily140 —
Domain ID domain_id6dqgD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
Domain ID domain_id6dqgD03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6dqgE01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily140 —
Domain ID domain_id6dqgE02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
Domain ID domain_id6dqgE03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
Domain ID domain_id6dqgF01
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology287 — Helix Hairpins
Homologous superfamily homologous superfamily140 —
Domain ID domain_id6dqgF02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily10860 — Leucine Dehydrogenase, chain A, domain 1
Domain ID domain_id6dqgF03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology50 — Rossmann fold
Homologous superfamily homologous superfamily720 — NAD(P)-binding Rossmann-like Domain
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8. Citations (1)

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9. Files and Curves (10)