6a9o

Rational discovery of a SOD1 tryptophan oxidation inhibitor with therapeutic potential for amyotrophic lateral sclerosis

Method: X-RAY DIFFRACTION Dmax: 141.1 Å Quality: REASONABLE

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

Superoxide dismutase [Cu-Zn]

Homo sapiens

UniProt P00441

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 × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 1–154 Chain B; UniProt 1–154 Not recorded ZN ZINC ION × 2 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 2 S4P Dihydrogen tetrasulfide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;1.5M Sodium Citrate, pH 6.0 Resolution 2.50 Å R-free 0.237
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain C; UniProt 1–154 Chain D; UniProt 1–154 Not recorded ZN ZINC ION × 2 DMS DIMETHYL SULFOXIDE × 1 GOL GLYCEROL × 2 S4P Dihydrogen tetrasulfide × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;1.5M Sodium Citrate, pH 6.0 Resolution 2.50 Å R-free 0.237
3 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain E; UniProt 1–154 Chain F; UniProt 1–154 Not recorded ZN ZINC ION × 2 S4P Dihydrogen tetrasulfide × 1 6B3 2'-[(6-oxo-5,6-dihydrophenanthridin-3-yl)carbamoyl][1,1'-biphenyl]-2-carboxylic acid × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;1.5M Sodium Citrate, pH 6.0 Resolution 2.50 Å R-free 0.237
4 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain G; UniProt 1–154 Chain H; UniProt 1–154 Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;1.5M Sodium Citrate, pH 6.0 Resolution 2.50 Å R-free 0.237
5 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain I; UniProt 1–154 Chain J; UniProt 1–154 Not recorded ZN ZINC ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;293 K;1.5M Sodium Citrate, pH 6.0 Resolution 2.50 Å R-free 0.237

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.

153 other PDB entries and 371 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name SODC_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 1–154; UniProt 1–154 Author chain B; PDBConstruct 1–154; UniProt 1–154 Author chain C; PDBConstruct 1–154; UniProt 1–154 Author chain D; PDBConstruct 1–154; UniProt 1–154 Author chain E; PDBConstruct 1–154; UniProt 1–154 Author chain F; PDBConstruct 1–154; UniProt 1–154 Author chain G; PDBConstruct 1–154; UniProt 1–154 Author chain H; PDBConstruct 1–154; UniProt 1–154 Author chain I; PDBConstruct 1–154; UniProt 1–154 Author chain J; PDBConstruct 1–154; UniProt 1–154

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 6a9o

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 6a9o
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2. Structure Basics 2. Structure Basics

Entry ID entry_id6a9o
Deposition date deposition_date2018-07-14
Structure title titleRational discovery of a SOD1 tryptophan oxidation inhibitor with therapeutic potential for amyotrophic lateral sclerosis
Keywords keywordsdismutase, dimer, oxidation, OXIDOREDUCTASE-INHIBITOR complex; OXIDOREDUCTASE/INHIBITOR
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier42.70
Radius of gyration Rg (electron density) rg_electron42.39
Forward intensity I(0) i0424389000.00
Molecular weight molecular_weight157420.0 kDa
Excluded volume excluded_volume192350 ų
Envelope volume envelope_volume273580 ų
Hydration-shell volume shell_volume54494 ų
Envelope diameter envelope_diameter149.6
Shell Rg shell_rg47.07
Envelope Rg envelope_rg41.34
Shape Rg shape_rg42.41
Total Rg total_rg42.54
Total atoms total_atoms11010
Residues n_residues1512
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 dmax141.1
Rg (real space) rg_real42.68
Rg uncertainty (real space) rg_real_error1.24
I(0) (real space) i0_real4.2440e+08
I(0) uncertainty (real space) i0_real_error7.3640e+06
Rg (reciprocal space) rg_reciprocal42.70
I(0) (reciprocal space) i0_reciprocal424400000.0000
Solution quality estimate total_estimate0.6704
Solution quality rating solution_quality REASONABLE a REASONABLE solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary53.4
Skewness Skewness skewness0.234
Kurtosis Kurtosis kurtosis-0.509
Angular range angular_range— – 0.1850 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha17500000.0000
Real-space data points n_real_points38
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.917; Stabil: 1.000; Sysdev: 0.016; Positv: 1.000; Valcen: 0.996; Smooth: 0.914

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (7)

7. Fold Classification (SCOP + CATH) 10 domains

SCOP 2.08 (10 domains)

Domain ID domain_idd6a9oa_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd6a9ob_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd6a9oc_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd6a9od_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd6a9oe_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd6a9of_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd6a9og_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd6a9oh_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd6a9oi_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like
Domain ID domain_idd6a9oj_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.8 — Cu,Zn superoxide dismutase-like
Family Family familyb.1.8.1 — Cu,Zn superoxide dismutase-like

8. Citations (1)

9. Files and Curves (10)