9qe3

Structure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and selenocyanate at pH 5.5

Method: X-RAY DIFFRACTION Dmax: 115.0 Å Quality: GOOD

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

Myeloperoxidase inhibitor SPIN

Staphylococcus aureus

UniProt Q2G0X2

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 6 其他Polymer 2 PDB declaration: hexameric(6) Consistent with protein copy count Chain E; UniProt 43–102 Chain F; UniProt 43–102 Not recorded Myeloperoxidase light chain × 2 (P05164) Myeloperoxidase heavy chain × 2 (P05164) ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 SEK SELENOCYANATE ION × 32 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;295.15 K;0.1 M Na Acet 5.5 pH (Buffer) 6 %(w/v) PEG 8K (Precipitant) 10 %(w/v) PEG 1K (Precipitant) 0.4 M KSeCN (Salt) Resolution 2.06 Å R-free 0.234

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.

5 other PDB entries and 6 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name Q2G0X2_STAA8
Isoform
PDB entities 1
Chains and sequence ranges Author chain E; PDBConstruct 1–60; UniProt 43–102 Author chain F; PDBConstruct 1–60; UniProt 43–102

Myeloperoxidase light chain

OrganismNot specified

UniProt P05164

State in the Current Structure

Assembly Oligomeric State Construct Mutations and Modifications Ligands, Ions and Associated Components Method and Experimental Conditions Structure Quality
1 Other combination Heteromer Protein × 6 其他Polymer 2 PDB declaration: hexameric(6) Consistent with protein copy count Chain A; UniProt 165–278 Chain B; UniProt 279–745 Chain C; UniProt 165–278 Chain D; UniProt 279–745 Fragment:UNP RESIDUES 167-271 Non-standard monomer:Yes (specific site not provided by mmCIF) Myeloperoxidase inhibitor SPIN × 2 (Q2G0X2) ;alpha-D-mannopyranose-(1-6)-beta-D-mannopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-[alpha-L-fucopyranose-(1-6)]2-acetamido-2-deoxy-beta-D-glucopyranose ; × 2 SEK SELENOCYANATE ION × 32 HEM PROTOPORPHYRIN IX CONTAINING FE × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4 CA CALCIUM ION × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, SITTING DROP;pH 5.5;295.15 K;0.1 M Na Acet 5.5 pH (Buffer) 6 %(w/v) PEG 8K (Precipitant) 10 %(w/v) PEG 1K (Precipitant) 0.4 M KSeCN (Salt) Resolution 2.06 Å R-free 0.234

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.

48 other PDB entries and 108 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name PERM_HUMAN
Isoform
PDB entities 2, 3
Chains and sequence ranges Author chain A; PDBConstruct 1–114; UniProt 165–278 Author chain C; PDBConstruct 1–114; UniProt 165–278 Author chain B; PDBConstruct 1–467; UniProt 279–745 Author chain D; PDBConstruct 1–467; UniProt 279–745

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 9qe3

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 9qe3
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2. Structure Basics 2. Structure Basics

Entry ID entry_id9qe3
Deposition date deposition_date2025-03-07
Structure title titleStructure of native leukocyte myeloperoxidase in complex with a truncated version of the Staphylococcal Peroxidase Inhibitor SPIN and selenocyanate at pH 5.5
Keywords keywordsInnate immunity, enzyme substrate complex, inhibitor, OXIDOREDUCTASE; OXIDOREDUCTASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier35.40
Radius of gyration Rg (electron density) rg_electron34.90
Forward intensity I(0) i0375616000.00
Molecular weight molecular_weight150400.0 kDa
Excluded volume excluded_volume184740 ų
Envelope volume envelope_volume224360 ų
Hydration-shell volume shell_volume52550 ų
Envelope diameter envelope_diameter119.3
Shell Rg shell_rg42.29
Envelope Rg envelope_rg35.00
Shape Rg shape_rg34.90
Total Rg total_rg35.37
Total atoms total_atoms20322
Residues n_residues1252
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 dmax115.0
Rg (real space) rg_real35.40
Rg uncertainty (real space) rg_real_error0.76
I(0) (real space) i0_real3.7560e+08
I(0) uncertainty (real space) i0_real_error5.3540e+06
Rg (reciprocal space) rg_reciprocal35.40
I(0) (reciprocal space) i0_reciprocal375600000.0000
Solution quality estimate total_estimate0.8904
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary38.4
Skewness Skewness skewness0.341
Kurtosis Kurtosis kurtosis-0.486
Angular range angular_range— – 0.2250 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha89360000.0000
Real-space data points n_real_points46
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.882; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.928

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (9)

8. Citations (1)

9. Files and Curves (10)