2onn

Arg475Gln Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Apo form

Method: X-RAY DIFFRACTION Dmax: 180.5 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 Mutation:R475Q No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.6;293 K;100 mM ACES (N-[2-Acetamido]-2-aminoethane sufonic acid), 10mM MgCl2, 100 mM Guanidine HCl, 16% w/v PEG 6000, 4 mM DTT, pH 6.6, vapor diffusion, temperature 293K Resolution 2.75 Å R-free 0.268
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 Mutation:R475Q No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION;pH 6.6;293 K;100 mM ACES (N-[2-Acetamido]-2-aminoethane sufonic acid), 10mM MgCl2, 100 mM Guanidine HCl, 16% w/v PEG 6000, 4 mM DTT, pH 6.6, vapor diffusion, temperature 293K Resolution 2.75 Å R-free 0.268

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 2onn

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 2onn
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2. Structure Basics 2. Structure Basics

Entry ID entry_id2onn
Deposition date deposition_date2007-01-24
Structure title titleArg475Gln Mutant of Human Mitochondrial Aldehyde Dehydrogenase, Apo form
Keywords keywordsoxidoreductase, ALDH, NAD, Rossmann Fold; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier61.86
Radius of gyration Rg (electron density) rg_electron62.32
Forward intensity I(0) i02569550000.00
Molecular weight molecular_weight431040.0 kDa
Excluded volume excluded_volume540340 ų
Envelope volume envelope_volume706010 ų
Hydration-shell volume shell_volume94777 ų
Envelope diameter envelope_diameter196.7
Shell Rg shell_rg61.12
Envelope Rg envelope_rg61.21
Shape Rg shape_rg62.30
Total Rg total_rg62.33
Total atoms total_atoms30368
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 dmax180.5
Rg (real space) rg_real62.27
Rg uncertainty (real space) rg_real_error1.45
I(0) (real space) i0_real2.5700e+09
I(0) uncertainty (real space) i0_real_error5.5350e+07
Rg (reciprocal space) rg_reciprocal61.43
I(0) (reciprocal space) i0_reciprocal2566000000.0000
Solution quality estimate total_estimate0.7919
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary50.5
Skewness Skewness skewness0.328
Kurtosis Kurtosis kurtosis-0.927
Angular range angular_range— – 0.1250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha218200000.0000
Real-space data points n_real_points26
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.799; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.895; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 24 domains

SCOP 2.08 (8 domains)

Domain ID domain_idd2onna_
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_idd2onnb_
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_idd2onnc_
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_idd2onnd_
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_idd2onne_
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_idd2onnf_
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_idd2onng_
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_idd2onnh_
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_id2onnA01
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_id2onnA02
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_id2onnB01
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_id2onnB02
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_id2onnC01
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_id2onnC02
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_id2onnD01
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_id2onnD02
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_id2onnE01
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_id2onnE02
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_id2onnF01
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_id2onnF02
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_id2onnG01
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_id2onnG02
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_id2onnH01
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_id2onnH02
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)