1cw3

HUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE COMPLEXED WITH NAD+ AND MN2+

Method: X-RAY DIFFRACTION Dmax: 167.2 Å Quality: GOOD

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

MITOCHONDRIAL 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 24–517 Chain B; UniProt 24–517 Chain C; UniProt 24–517 Chain D; UniProt 24–517 Fragment:COMPLETE MATURE SEQUENCE (DOES NOT INCLUDE MITOCHONDRIAL LEADER SEQUENCE) MN MANGANESE (II) ION × 4 MG MAGNESIUM ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.4;293 K;100 MM ACES, PH 6.4, 100 MM GUANIDINE-HCL, 2 MM NAD+, 4 MM DTT, 16% PEG 6000, 8 MG/ML ENZYME SOAKED WITH 8 MM MNCL2 FOR 2 DAYS, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.58 Å R-free 0.242
2 Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric(4) Consistent with protein copy count Chain E; UniProt 24–517 Chain F; UniProt 24–517 Chain G; UniProt 24–517 Chain H; UniProt 24–517 Fragment:COMPLETE MATURE SEQUENCE (DOES NOT INCLUDE MITOCHONDRIAL LEADER SEQUENCE) MN MANGANESE (II) ION × 4 MG MAGNESIUM ION × 4 NAD NICOTINAMIDE-ADENINE-DINUCLEOTIDE × 4 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 6.4;293 K;100 MM ACES, PH 6.4, 100 MM GUANIDINE-HCL, 2 MM NAD+, 4 MM DTT, 16% PEG 6000, 8 MG/ML ENZYME SOAKED WITH 8 MM MNCL2 FOR 2 DAYS, VAPOR DIFFUSION, SITTING DROP, temperature 293K Resolution 2.58 Å R-free 0.242

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 1–494; UniProt 24–517 Author chain B; PDBConstruct 1–494; UniProt 24–517 Author chain C; PDBConstruct 1–494; UniProt 24–517 Author chain D; PDBConstruct 1–494; UniProt 24–517 Author chain E; PDBConstruct 1–494; UniProt 24–517 Author chain F; PDBConstruct 1–494; UniProt 24–517 Author chain G; PDBConstruct 1–494; UniProt 24–517 Author chain H; PDBConstruct 1–494; UniProt 24–517

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 1cw3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 1cw3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id1cw3
Deposition date deposition_date1999-08-25
Structure title titleHUMAN MITOCHONDRIAL ALDEHYDE DEHYDROGENASE COMPLEXED WITH NAD+ AND MN2+
Keywords keywordsDINUCLEOTIDE FOLD, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier53.96
Radius of gyration Rg (electron density) rg_electron54.16
Forward intensity I(0) i02728590000.00
Molecular weight molecular_weight437220.0 kDa
Excluded volume excluded_volume546240 ų
Envelope volume envelope_volume675780 ų
Hydration-shell volume shell_volume103630 ų
Envelope diameter envelope_diameter182.0
Shell Rg shell_rg56.52
Envelope Rg envelope_rg53.78
Shape Rg shape_rg54.15
Total Rg total_rg54.27
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 dmax167.2
Rg (real space) rg_real54.20
Rg uncertainty (real space) rg_real_error1.39
I(0) (real space) i0_real2.7290e+09
I(0) uncertainty (real space) i0_real_error5.4110e+07
Rg (reciprocal space) rg_reciprocal53.75
I(0) (reciprocal space) i0_reciprocal2727000000.0000
Solution quality estimate total_estimate0.8229
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary51.9
Skewness Skewness skewness0.493
Kurtosis Kurtosis kurtosis-0.382
Angular range angular_range— – 0.1450 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha320400000.0000
Real-space data points n_real_points30
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.897; Stabil: 0.998; Sysdev: 1.000; Positv: 1.000; Valcen: 1.000; Smooth: 0.007

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_idd1cw3a_
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_idd1cw3b_
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_idd1cw3c_
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_idd1cw3d_
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_idd1cw3e_
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_idd1cw3f_
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_idd1cw3g_
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_idd1cw3h_
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_id1cw3A01
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_id1cw3A02
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_id1cw3B01
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_id1cw3B02
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_id1cw3C01
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_id1cw3C02
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_id1cw3D01
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_id1cw3D02
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_id1cw3E01
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_id1cw3E02
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_id1cw3F01
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_id1cw3F02
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_id1cw3G01
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_id1cw3G02
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_id1cw3H01
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_id1cw3H02
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 (2)

9. Files and Curves (10)