1nzz

Human mitochondrial aldehyde dehydrogenase complexed with NADH in the presence of low Mg2+

Method: X-RAY DIFFRACTION Dmax: 179.2 Å Quality: GOOD

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

Aldehyde dehydrogenase

Homo sapiens

UniProt P05091

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 × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain A; UniProt 18–517 Chain B; UniProt 18–517 Chain C; UniProt 18–517 Chain D; UniProt 18–517 Fragment:Complete mature sequence (does not contain mitochondrial leader sequence). NA SODIUM ION × 4 MG MAGNESIUM ION × 4 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.4;293 K;ACES, PEG 6000, Guanidine HCl, MgCl2, DTT. Crystal soaked at increasing pH and decreasing concentrations of Mg2+ and then with NADH and 0.2 mM Mg2+ at pH 7.0 prior to data collection., pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.45 Å R-free 0.248
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 18–517 Chain F; UniProt 18–517 Chain G; UniProt 18–517 Chain H; UniProt 18–517 Fragment:Complete mature sequence (does not contain mitochondrial leader sequence). NA SODIUM ION × 4 MG MAGNESIUM ION × 4 NAI 1,4-DIHYDRONICOTINAMIDE ADENINE DINUCLEOTIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.4;293 K;ACES, PEG 6000, Guanidine HCl, MgCl2, DTT. Crystal soaked at increasing pH and decreasing concentrations of Mg2+ and then with NADH and 0.2 mM Mg2+ at pH 7.0 prior to data collection., pH 6.4, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.45 Å R-free 0.248

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.

28 other PDB entries and 59 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name ALDH2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–500; UniProt 18–517 Author chain B; PDBConstruct 1–500; UniProt 18–517 Author chain C; PDBConstruct 1–500; UniProt 18–517 Author chain D; PDBConstruct 1–500; UniProt 18–517 Author chain E; PDBConstruct 1–500; UniProt 18–517 Author chain F; PDBConstruct 1–500; UniProt 18–517 Author chain G; PDBConstruct 1–500; UniProt 18–517 Author chain H; PDBConstruct 1–500; UniProt 18–517

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 1nzz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1nzz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1nzz
Deposition date deposition_date2003-02-20
Structure title titleHuman mitochondrial aldehyde dehydrogenase complexed with NADH in the presence of low Mg2+
Keywords keywordsALDH, NAD, NADH, isomerization, Oxidoreductase; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier61.83
Radius of gyration Rg (electron density) rg_electron62.28
Forward intensity I(0) i02677090000.00
Molecular weight molecular_weight436980.0 kDa
Excluded volume excluded_volume546420 ų
Envelope volume envelope_volume700100 ų
Hydration-shell volume shell_volume94062 ų
Envelope diameter envelope_diameter196.9
Shell Rg shell_rg61.06
Envelope Rg envelope_rg61.16
Shape Rg shape_rg62.27
Total Rg total_rg62.30
Total atoms total_atoms30752
Residues n_residues3952
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −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

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

Maximum dimension Dmax dmax179.2
Rg (real space) rg_real62.23
Rg uncertainty (real space) rg_real_error1.55
I(0) (real space) i0_real2.6770e+09
I(0) uncertainty (real space) i0_real_error5.6300e+07
Rg (reciprocal space) rg_reciprocal61.40
I(0) (reciprocal space) i0_reciprocal2673000000.0000
Solution quality estimate total_estimate0.7891
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.2
Skewness Skewness skewness0.321
Kurtosis Kurtosis kurtosis-0.940
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha189900000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.792; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.879; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (5)

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd1nzza_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.82 — ALDH-like
Superfamily Superfamily superfamilyc.82.1 — ALDH-like
Family Family familyc.82.1.1 — ALDH-like
Domain ID domain_idd1nzzb_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.82 — ALDH-like
Superfamily Superfamily superfamilyc.82.1 — ALDH-like
Family Family familyc.82.1.1 — ALDH-like
Domain ID domain_idd1nzzc_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.82 — ALDH-like
Superfamily Superfamily superfamilyc.82.1 — ALDH-like
Family Family familyc.82.1.1 — ALDH-like
Domain ID domain_idd1nzzd_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.82 — ALDH-like
Superfamily Superfamily superfamilyc.82.1 — ALDH-like
Family Family familyc.82.1.1 — ALDH-like
Domain ID domain_idd1nzze_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.82 — ALDH-like
Superfamily Superfamily superfamilyc.82.1 — ALDH-like
Family Family familyc.82.1.1 — ALDH-like
Domain ID domain_idd1nzzf_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.82 — ALDH-like
Superfamily Superfamily superfamilyc.82.1 — ALDH-like
Family Family familyc.82.1.1 — ALDH-like
Domain ID domain_idd1nzzg_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.82 — ALDH-like
Superfamily Superfamily superfamilyc.82.1 — ALDH-like
Family Family familyc.82.1.1 — ALDH-like
Domain ID domain_idd1nzzh_
Class classc — Alpha and beta proteins (a/b)
Fold Fold foldc.82 — ALDH-like
Superfamily Superfamily superfamilyc.82.1 — ALDH-like
Family Family familyc.82.1.1 — ALDH-like

CATH v4.4 (16 domains)

Domain ID domain_id1nzzA01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 1
Domain ID domain_id1nzzA02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 2
Domain ID domain_id1nzzB01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 1
Domain ID domain_id1nzzB02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 2
Domain ID domain_id1nzzC01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 1
Domain ID domain_id1nzzC02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 2
Domain ID domain_id1nzzD01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 1
Domain ID domain_id1nzzD02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 2
Domain ID domain_id1nzzE01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 1
Domain ID domain_id1nzzE02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 2
Domain ID domain_id1nzzF01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 1
Domain ID domain_id1nzzF02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 2
Domain ID domain_id1nzzG01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 1
Domain ID domain_id1nzzG02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 2
Domain ID domain_id1nzzH01
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology605 — Aldehyde Dehydrogenase; Chain A, domain 1
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 1
Domain ID domain_id1nzzH02
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology309 — Aldehyde Dehydrogenase; Chain A, domain 2
Homologous superfamily homologous superfamily10 — Aldehyde Dehydrogenase; Chain A, domain 2

8. Citations (1)

9. Files and Curves (10)