SAXSdb — 1nhl

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

Synaptosomal-associated protein 23

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 23–76	Fragment：SNAP-23 N-terminal coiled-coil domain Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；HEPES, CALCIUM CHLORIDE, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.316
2	Protein homooligomer Homooligomer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 23–76	Fragment：SNAP-23 N-terminal coiled-coil domain Non-standard monomer：Yes (specific site not provided by mmCIF)	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 7.5；298 K；HEPES, CALCIUM CHLORIDE, PEG 400, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K	Resolution 2.30 Å R-free 0.316

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 1NHL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ZUS Crystal structure of an engineered botulinum neurotoxin type A- SNARE23 derivative, LC-A-SNAP23-Hn-A Deposited 2011-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain A 150–211（62 aa） Fragment：LC-A-SNAP23-HN-A, LC-A, RESIDUES 3-431,SNAP23,RESIDUES 150-211,8-RESIDUE LINKER, HN-A, RESIDUES 454-865	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.1 M IMIDAZOLE MALATE PH 6.0, 15% PEG 3350.	Resolution 2.95 Å R-free 0.293
3ZUS Crystal structure of an engineered botulinum neurotoxin type A- SNARE23 derivative, LC-A-SNAP23-Hn-A Deposited 2011-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain B 150–211（62 aa） Fragment：LC-A-SNAP23-HN-A, LC-A, RESIDUES 3-431,SNAP23,RESIDUES 150-211,8-RESIDUE LINKER, HN-A, RESIDUES 454-865	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.1 M IMIDAZOLE MALATE PH 6.0, 15% PEG 3350.	Resolution 2.95 Å R-free 0.293
3ZUS Crystal structure of an engineered botulinum neurotoxin type A- SNARE23 derivative, LC-A-SNAP23-Hn-A Deposited 2011-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain C 150–211（62 aa） Fragment：LC-A-SNAP23-HN-A, LC-A, RESIDUES 3-431,SNAP23,RESIDUES 150-211,8-RESIDUE LINKER, HN-A, RESIDUES 454-865	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.1 M IMIDAZOLE MALATE PH 6.0, 15% PEG 3350.	Resolution 2.95 Å R-free 0.293
3ZUS Crystal structure of an engineered botulinum neurotoxin type A- SNARE23 derivative, LC-A-SNAP23-Hn-A Deposited 2011-07-19	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Insufficient information Monomer；Protein × 1 PDB declaration: monomeric	Chain D 150–211（62 aa） Fragment：LC-A-SNAP23-HN-A, LC-A, RESIDUES 3-431,SNAP23,RESIDUES 150-211,8-RESIDUE LINKER, HN-A, RESIDUES 454-865	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6；0.1 M IMIDAZOLE MALATE PH 6.0, 15% PEG 3350.	Resolution 2.95 Å R-free 0.293

1 other PDB entries and 4 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SNP23_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–54； UniProt 23–76

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	1nhl
Deposition date deposition_date	2002-12-19
Structure title title	SNAP-23N Structure
Keywords keywords	SNARE, COILED-COIL, PROTEIN TRANSPORT; PROTEIN TRANSPORT
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	22.08 Å
Radius of gyration Rg (electron density) rg_electron	23.55 Å
Forward intensity I(0) i0	964400.00
Molecular weight molecular_weight	6309.0 kDa
Excluded volume excluded_volume	7713 Å³
Envelope volume envelope_volume	11503 Å³
Hydration-shell volume shell_volume	5902 Å³
Envelope diameter envelope_diameter	83.8 Å
Shell Rg shell_rg	23.18 Å
Envelope Rg envelope_rg	24.35 Å
Shape Rg shape_rg	23.55 Å
Total Rg total_rg	23.48 Å
Total atoms total_atoms	433
Residues n_residues	52
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	85.0 Å
Rg (real space) rg_real	23.02 Å
Rg uncertainty (real space) rg_real_error	1.36 Å
I(0) (real space) i0_real	9.6440e+05
I(0) uncertainty (real space) i0_real_error	1.4090e+04
Rg (reciprocal space) rg_reciprocal	22.85 Å
I(0) (reciprocal space) i0_reciprocal	964300.0000
Solution quality estimate total_estimate	0.6176
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	4
Primary peak position r_peak_primary	10.2 Å
Skewness Skewness skewness	0.707
Kurtosis Kurtosis kurtosis	-0.253
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	30040.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.041; Stabil: 0.996; Sysdev: 1.000; Positv: 1.000; Valcen: 0.004; Smooth: 0.909

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d1nhla_
Class class	h — Coiled coil proteins
Fold Fold fold	h.1 — Parallel coiled-coil
Superfamily Superfamily superfamily	h.1.15 — SNARE fusion complex
Family Family family	h.1.15.1 — SNARE fusion complex

CATH v4.4 (1 domains)

Domain ID domain_id	1nhlA00
Class class	1 — Mainly Alpha
Architecture architecture	20 — Up-down Bundle
Topology topology	5 — Single alpha-helices involved in coiled-coils or other helix-helix interfaces
Homologous superfamily homologous superfamily	110 —

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8. Citations (1)

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Unit-cell length a length_a	34.905 Å
Unit-cell length b length_b	34.905 Å
Unit-cell length c length_c	81.691 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 4 21 2
Space-group number int_tables_number	90
Crystal system crystal_system	—

Resolution resolution	2.300 Å
Low-resolution limit resolution_low	20.000 Å
R factor r_factor	0.2770
R_work r_work	0.2730
R_free r_free	0.3160

Description description	Synaptosomal-associated protein 23
Molecular weight formula_weight	6318.8 kDa
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	476

SNAP-23N Structure

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

Synaptosomal-associated protein 23

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 water

7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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 BL21(DE3)

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	43

fit	/app/data/saxs_computation/nh/1nhl/1nhl.fit
pddf	/app/data/pr_computation/nh/1nhl/1nhl.pr.out
profile	/app/data/saxs_computation/nh/1nhl/1nhl.dat