SAXSdb — 8vjy

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

Neurolysin, mitochondrial

Homo sapiens

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 38–704	Non-standard monomer：Yes (specific site not provided by mmCIF)	Neurotensin × 1 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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain C； UniProt 38–704	Non-standard monomer：Yes (specific site not provided by mmCIF)	Neurotensin × 1 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

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 8VJY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5LUZ Structure of Human Neurolysin (E475Q) in complex with neurotensin peptide products Deposited 2016-09-12	Different mutation/modification Different oligomeric state 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）	Mutation：E475Q	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
5LUZ Structure of Human Neurolysin (E475Q) in complex with neurotensin peptide products Deposited 2016-09-12	Different mutation/modification Different oligomeric state 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）	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 0.268
5LV0 Structure of Human Neurolysin (E475Q) in complex with amyloid-beta 35-40 peptide product Deposited 2016-09-12	Different mutation/modification 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）	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 mutation/modification Different ligand/ion Different experimental conditions 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 ligand/ion 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 ligand/ion 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 oligomeric state Different ligand/ion 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 oligomeric state Different ligand/ion 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 ligand/ion 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

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 1–667； UniProt 38–704 Author chain C； PDBConstruct 1–667； 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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	8vjy
Deposition date deposition_date	2024-01-08
Structure title title	Structure of Human Neurolysin in complex with Neurotensin peptide
Keywords keywords	metallopeptidase, bioactive peptides, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier	37.17 Å
Radius of gyration Rg (electron density) rg_electron	36.75 Å
Forward intensity I(0) i0	364365000.00
Molecular weight molecular_weight	156110.0 kDa
Excluded volume excluded_volume	195710 Å³
Envelope volume envelope_volume	244610 Å³
Hydration-shell volume shell_volume	54718 Å³
Envelope diameter envelope_diameter	127.3 Å
Shell Rg shell_rg	43.82 Å
Envelope Rg envelope_rg	36.25 Å
Shape Rg shape_rg	36.72 Å
Total Rg total_rg	37.29 Å
Total atoms total_atoms	10946
Residues n_residues	1342
Spherical-harmonic order n_harmonics	20
q range q_range	— – 0.5000 Å⁻¹
Data points n_points	101
Shell type shell_type	directional
Solvent electron density solvent_density	0.3340 e/Å³
Shell contrast contrast_shell	0.0300 e/Å³
CRYSOL version crysol_version	4.1.3

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4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax	120.8 Å
Rg (real space) rg_real	37.16 Å
Rg uncertainty (real space) rg_real_error	1.03 Å
I(0) (real space) i0_real	3.6440e+08
I(0) uncertainty (real space) i0_real_error	6.2970e+06
Rg (reciprocal space) rg_reciprocal	37.17 Å
I(0) (reciprocal space) i0_reciprocal	364400000.0000
Solution quality estimate total_estimate	0.8896
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	39.3 Å
Skewness Skewness skewness	0.303
Kurtosis Kurtosis kurtosis	-0.560
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	122400000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.890; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.905

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Description description	Neurolysin, mitochondrial
Molecular weight formula_weight	76688.7 kDa
EC 编号 ec_number	3.4.24.16
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,C
Atom count atom_count	12083

SSYTVAGRNVLRWDLSPEQIKTRTEELIVQTKQVYDAVGMLGIEEVTYENCLQALADVEVKYIVERTMLDFPQHVSSDKEVRAASTEADKRLSRFDIEMSMRGDIFERIVHLQETCDLGKIKPEARRYLEKSIKMGKRNGLHLPEQVQNEIKSMKKRMSELCIDFNKNLNEDDTFLVFSKAELGALPDDFIDSLEKTDDDKYKITLKYPHYFPVMKKCCIPETRRRMEMAFNTRCKEENTIILQQLLPLRTKVAKLLGYSTHADFVLEMNTAKSTSRVTAFLDDLSQKLKPLGEAEREFILNLKKKECKDRGFEYDGKINAWDLYYYMTQTEELKYSIDQEFLKEYFPIEVVTEGLLNTYQELLGLSFEQMTDAHVWNKSVTLYTVKDKATGEVLGQFYLDLYPREGKYNHAACFGLQPGCLLPDGSRMMAVAALVVNFSQPVAGRPSLLRHDEVRTYFHEFGHVMHQICAQTDFARFSGTNVETDFVEVPSQMLENWVWDVDSLRRLSKHYKDGSPIADDLLEKLVASRLVNTGLLTLRQIVLSKVDQSLHTNTSLDAASEYAKYCSEILGVAATPGTNMPATFGHLAGGYDGQYYGYLWSEVFSMDMFYSCFKKEGIMNPEVGMKYRNLILKPGGSLDGMDMLHNFLKREPNQKAFLMSRGLHAP

来源 Source

来源生物 organism	Homo sapiens
通用名 common_name	human
NCBI Class编号 ncbi_taxonomy_id	9606
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 polymer

Description description	Neurotensin
Molecular weight formula_weight	1790.1 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,D

PQLYENKPRRPYIL

Entity 3 Entity 3 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	2

Entity 4 Entity 4 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	22

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	989

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8. Citations (1)

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Unit-cell length a length_a	59.712 Å
Unit-cell length b length_b	150.576 Å
Unit-cell length c length_c	188.799 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	8

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.950 Å
Low-resolution limit resolution_low	48.510 Å
R factor r_factor	0.1994
R_work r_work	0.1976
R_free r_free	0.2338

fit	/app/data/saxs_computation/vj/8vjy/8vjy.fit
pddf	/app/data/pr_computation/vj/8vjy/8vjy.pr.out
profile	/app/data/saxs_computation/vj/8vjy/8vjy.dat

Structure of Human Neurolysin in complex with Neurotensin peptide

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

Neurolysin, mitochondrial

State in the Current Structure

Other States of the Same Protein in the Database

SAXS scattering curve SAXS Profile

P(r) Distance Distribution P(r) Distribution

2. Structure Basics 2. Structure Basics

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

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

5. Crystallography and Experiment 5. Crystallography & Experiment

Unit cell Unit Cell

Symmetry Symmetry

Refinement Refinement

Diffraction experiment Diffraction

6. Entities and Polymers Entities & Polymers (5)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)