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5luz

Structure of Human Neurolysin (E475Q) in complex with neurotensin peptide products

Method: X-RAY DIFFRACTION Dmax: 121.8 Å Quality: GOOD
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1. Protein Identity and Related Structures Protein Identity & Related Structures

Neurolysin, mitochondrial

Homo sapiens

UniProt Q9BYT8

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 heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain A； UniProt 38–704 Mutation：E475Q PRO-ARG-ARG-PRO neurotensin fragment × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1M Bis-Tris-propane, 11% PEG 3350, 10% glycerol, 0.2M potassium thiocyanate Resolution 2.70 Å R-free 0.268
2 Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count Chain B； UniProt 38–704 Mutation：E475Q PRO-ARG-ARG-PRO neurotensin fragment × 2 ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1M Bis-Tris-propane, 11% PEG 3350, 10% glycerol, 0.2M potassium thiocyanate Resolution 2.70 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.

Other PDB Difference from Current Entry 5LUZ Assembly / Oligomeric State Construct Mutations and Modifications Ligands, Ions and Non-polymers Method and Experimental Conditions Structure Quality
5LV0 Structure of Human Neurolysin (E475Q) in complex with amyloid-beta 35-40 peptide product Deposited 2016-09-12 Different oligomeric state Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 38–704（667 aa）
Mutation：E475Q ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1M Bis-Tris-propane, 11% PEG 3350, 10% glycerol, 0.2M potassium thiocyanate
Resolution 2.70 Å R-free 0.260
5LV0 Structure of Human Neurolysin (E475Q) in complex with amyloid-beta 35-40 peptide product Deposited 2016-09-12 Different oligomeric state Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain B 38–704（667 aa）
Mutation：E475Q ZN ZINC ION × 1 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；294 K；0.1M Bis-Tris-propane, 11% PEG 3350, 10% glycerol, 0.2M potassium thiocyanate
Resolution 2.70 Å R-free 0.260
8VJU Structure of Human Neurolysin in complex with dynorphin A13 peptide Deposited 2024-01-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 38–704（667 aa）
Not recorded ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 8 CL CHLORIDE ION × 1 NA SODIUM ION × 2 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 1.99 Å R-free 0.218
8VJV Structure of Human Neurolysin in complex with dynorphin A8(1-8) peptide Deposited 2024-01-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 38–704（667 aa）
Not recorded ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 3 CL CHLORIDE ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 2.12 Å R-free 0.249
8VJW Structure of Human Neurolysin in complex with angiotensin I peptide Deposited 2024-01-08 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain A 38–704（667 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 2.49 Å R-free 0.286
8VJW Structure of Human Neurolysin in complex with angiotensin I peptide Deposited 2024-01-08 Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric
Chain B 38–704（667 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 2.49 Å R-free 0.286
8VJX Structure of Human Neurolysin in complex with bradykinin peptide Deposited 2024-01-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 38–704（667 aa）
Not recorded ZN ZINC ION × 1 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 2.89 Å R-free 0.255
8VJY Structure of Human Neurolysin in complex with Neurotensin peptide Deposited 2024-01-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain A 38–704（667 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 12 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 1.95 Å R-free 0.234
8VJY Structure of Human Neurolysin in complex with Neurotensin peptide Deposited 2024-01-08 Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric
Chain C 38–704（667 aa）
Non-standard monomer：Yes (specific site not provided by mmCIF) ZN ZINC ION × 1 EDO 1,2-ETHANEDIOL × 10 X-RAY DIFFRACTION
X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；17.5 ~ 30 % polyethylene glycol 3,350 and 50 ~ 125 mM Bis-Tris HCl buffer, pH 6.5
Resolution 1.95 Å R-free 0.234

6 other PDB entries and 9 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name NEUL_HUMAN
Isoform —
PDB entities 1
Chains and sequence ranges Author chain A； PDBConstruct 20–686； UniProt 38–704 Author chain B； PDBConstruct 20–686； UniProt 38–704

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 5luz

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 5luz
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2. Structure Basics 2. Structure Basics

Entry ID entry_id5luz
Deposition date deposition_date2016-09-12
Structure title titleStructure of Human Neurolysin (E475Q) in complex with neurotensin peptide products
Keywords keywordsPROTEASE, MITOCHONDRIA, HYDROLASE, NEUROTENSIN; HYDROLASE
Experimental Method methodX-RAY DIFFRACTION
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3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier37.47 Å
Radius of gyration Rg (electron density) rg_electron37.21 Å
Forward intensity I(0) i0356183000.00
Molecular weight molecular_weight154410.0 kDa
Excluded volume excluded_volume193450 ų
Envelope volume envelope_volume247420 ų
Hydration-shell volume shell_volume54450 ų
Envelope diameter envelope_diameter122.2 Å
Shell Rg shell_rg44.40 Å
Envelope Rg envelope_rg36.77 Å
Shape Rg shape_rg37.22 Å
Total Rg total_rg37.59 Å
Total atoms total_atoms10833
Residues n_residues1342
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 Å−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
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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax121.8 Å
Rg (real space) rg_real37.48 Å
Rg uncertainty (real space) rg_real_error0.86 Å
I(0) (real space) i0_real3.5620e+08
I(0) uncertainty (real space) i0_real_error6.6030e+06
Rg (reciprocal space) rg_reciprocal37.48 Å
I(0) (reciprocal space) i0_reciprocal356200000.0000
Solution quality estimate total_estimate0.8870
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks1
Primary peak position r_peak_primary37.7 Å
Skewness Skewness skewness0.314
Kurtosis Kurtosis kurtosis-0.592
Angular range angular_range— – 0.2100 Å−1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha158900000.0000
Real-space data points n_real_points43
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.881; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.885
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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (6)

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7. Fold Classification (SCOP + CATH) 6 domains

CATH v4.4 (6 domains)

Domain ID domain_id5luzA01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily40 — Endopeptidase. Chain P; domain 1
Domain ID domain_id5luzA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1370 — Neurolysin; domain 3
Homologous superfamily homologous superfamily10 — Neurolysin, domain 3
Domain ID domain_id5luzA03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
Domain ID domain_id5luzB01
Class class1 — Mainly Alpha
Architecture architecture20 — Up-down Bundle
Topology topology1050 — Glutathione S-transferase Yfyf (Class Pi); Chain A, domain 2
Homologous superfamily homologous superfamily40 — Endopeptidase. Chain P; domain 1
Domain ID domain_id5luzB02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology1370 — Neurolysin; domain 3
Homologous superfamily homologous superfamily10 — Neurolysin, domain 3
Domain ID domain_id5luzB03
Class class3 — Alpha Beta
Architecture architecture40 — 3-Layer(aba) Sandwich
Topology topology390 — Collagenase (Catalytic Domain)
Homologous superfamily homologous superfamily10 — Collagenase (Catalytic Domain)
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8. Citations (1)

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9. Files and Curves (10)