SAXSdb — 5z6r

▼

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

Spastin

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 229–616	Fragment：UNP RESIDUES 229-616 Mutation：E442Q	ATP ADENOSINE-5'-TRIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 8.2；293 K；25MM TRIS-HCL, 1MM DTT, 1MM MGCL2, 1MM ATP, 2% PEG 3350, 20MM KSCN	Resolution 3.00 Å R-free 0.279

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 5Z6R	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3EAB Crystal structure of Spastin MIT in complex with ESCRT III Deposited 2008-08-25	Different construct 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 112–196（85 aa） Fragment：UNP residues 112 to 196	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；288 K；10% PEG 2000 MME, 0.2 M Ammonia Sulfate, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.50 Å R-free 0.268
3EAB Crystal structure of Spastin MIT in complex with ESCRT III Deposited 2008-08-25	Different construct 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 B 112–196（85 aa） Fragment：UNP residues 112 to 196	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；288 K；10% PEG 2000 MME, 0.2 M Ammonia Sulfate, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.50 Å R-free 0.268
3EAB Crystal structure of Spastin MIT in complex with ESCRT III Deposited 2008-08-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain C 112–196（85 aa） Fragment：UNP residues 112 to 196	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；288 K；10% PEG 2000 MME, 0.2 M Ammonia Sulfate, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.50 Å R-free 0.268
3EAB Crystal structure of Spastin MIT in complex with ESCRT III Deposited 2008-08-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain D 112–196（85 aa） Fragment：UNP residues 112 to 196	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；288 K；10% PEG 2000 MME, 0.2 M Ammonia Sulfate, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.50 Å R-free 0.268
3EAB Crystal structure of Spastin MIT in complex with ESCRT III Deposited 2008-08-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 5 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain E 112–196（85 aa） Fragment：UNP residues 112 to 196	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；288 K；10% PEG 2000 MME, 0.2 M Ammonia Sulfate, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.50 Å R-free 0.268
3EAB Crystal structure of Spastin MIT in complex with ESCRT III Deposited 2008-08-25	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 6 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain F 112–196（85 aa） Fragment：UNP residues 112 to 196	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；288 K；10% PEG 2000 MME, 0.2 M Ammonia Sulfate, 0.1 M Sodium Acetate, pH 4.6, VAPOR DIFFUSION, HANGING DROP, temperature 288K	Resolution 2.50 Å R-free 0.268
3VFD Human spastin AAA domain Deposited 2012-01-09	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 228–616（389 aa） Fragment：AAA domain	Mutation：E442Q	SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；296 K；1.6M (NH3)2SO4, 0.1M MES monohydrate (pH 6.5),10% 1,4-dioxane and 4% benzamidine HCl, 1mM ATP, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 3.30 Å R-free 0.275
5Z6Q Crystal structure of AAA of Spastin Deposited 2018-01-25	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 229–616（388 aa） Fragment：UNP residues 229-616	Not recorded	CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；3M (NH4)2SO4, 100mM NH4Cl	Resolution 3.00 Å R-free 0.276
6PEK Structure of Spastin Hexamer (Subunit A-E) in complex with substrate peptide Deposited 2019-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 87–584（498 aa） Chain B 87–584（498 aa） Chain C 87–584（498 aa） Chain D 87–584（498 aa） Chain E 87–584（498 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 BEF BERYLLIUM TRIFLUORIDE ION × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
6PEN Structure of Spastin Hexamer (whole model) in complex with substrate peptide Deposited 2019-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 7 PDB declaration: heptameric	Chain A 87–584（498 aa） Chain B 87–584（498 aa） Chain C 87–584（498 aa） Chain D 87–584（498 aa） Chain E 87–584（498 aa） Chain F 87–584（498 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 5 BEF BERYLLIUM TRIFLUORIDE ION × 4 MG MAGNESIUM ION × 4	ELECTRON MICROSCOPY cryo-EM buffer pH 8 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 4.20 Å
7S7J Structure of Human SPASTIN-IST1 complex. Deposited 2021-09-16	Different construct 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 112–195（84 aa）	Not recorded	PG4 TETRAETHYLENE GLYCOL × 1 CA CALCIUM ION × 1 PGE TRIETHYLENE GLYCOL × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 6.5；278 K；40% v/v PEG 300, 100 mM Sodium cacodylate / Hydrochloric acid pH=6.5, 200 mM Calcium Acetate	Resolution 1.15 Å R-free 0.157

6 other PDB entries and 11 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	SPAST_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–392； UniProt 229–616

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.

▼

2. Structure Basics 2. Structure Basics

Entry ID entry_id	5z6r
Deposition date deposition_date	2018-01-25
Structure title title	SPASTIN AAA WITH ATP
Keywords keywords	SPASTIN, HYDROLASE; HYDROLASE
Experimental Method method	X-RAY DIFFRACTION

▼

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	21.28 Å
Forward intensity I(0) i0	14687800.00
Molecular weight molecular_weight	28775.0 kDa
Excluded volume excluded_volume	36065 Å³
Envelope volume envelope_volume	44526 Å³
Hydration-shell volume shell_volume	18255 Å³
Envelope diameter envelope_diameter	75.8 Å
Shell Rg shell_rg	26.98 Å
Envelope Rg envelope_rg	21.71 Å
Shape Rg shape_rg	21.28 Å
Total Rg total_rg	22.10 Å
Total atoms total_atoms	2022
Residues n_residues	273
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

▼

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

Maximum dimension Dmax dmax	73.1 Å
Rg (real space) rg_real	22.18 Å
Rg uncertainty (real space) rg_real_error	0.59 Å
I(0) (real space) i0_real	1.4690e+07
I(0) uncertainty (real space) i0_real_error	2.1810e+05
Rg (reciprocal space) rg_reciprocal	22.16 Å
I(0) (reciprocal space) i0_reciprocal	14690000.0000
Solution quality estimate total_estimate	0.7957
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.8 Å
Skewness Skewness skewness	0.439
Kurtosis Kurtosis kurtosis	-0.357
Angular range angular_range	— – 0.3600 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	3074000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.818; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.887; Smooth: 0.000

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	Spastin
Molecular weight formula_weight	42743.8 kDa
EC 编号 ec_number	3.6.4.3
Mutation mutation	E442Q
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	2022

GPGSSGAVPKRKDPLTHTSNSLPRSKTVMKTGSAGLSGHHRAPSYSGLSMVSGVKQGSGPAPTTHKGTPKTNRTNKPSTPTTATRKKKDLKNFRNVDSNLANLIMNEIVDNGTAVKFDDIAGQDLAKQALQEIVILPSLRPELFTGLRAPARGLLLFGPPGNGKTMLAKAVAAESNATFFNISAASLTSKYVGEGEKLVRALFAVARELQPSIIFIDQVDSLLCERREGEHDASRRLKTEFLIEFDGVQSAGDDRVLVMGATNRPQELDEAVLRRFIKRVYVSLPNEETRLLLLKNLLCKQGSPLTQKELAQLARMTDGYSGSDLTALAKDAALGPIRELKPEQVKNMSASEMRNIRLSDFTESLKKIKRSVSPQTLEAYIRWNKDFGDTTV

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 'BL21-Gold(DE3)pLysS AG' ;

Entity 2 Entity 2 non-polymer

Description description	ADENOSINE-5'-TRIPHOSPHATE
Molecular weight formula_weight	507.2 kDa
Source method src_method	syn
Copy count entity_count	1

▼

7. Fold Classification (SCOP + CATH) 1 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d5z6ra_
Class class	c — Alpha and beta proteins (a/b)
Fold Fold fold	c.37 — P-loop containing nucleoside triphosphate hydrolases
Superfamily Superfamily superfamily	c.37.1 — P-loop containing nucleoside triphosphate hydrolases
Family Family family	c.37.1.0 — automated matches

▶

8. Citations (1)

▶

Unit-cell length a length_a	87.257 Å
Unit-cell length b length_b	87.257 Å
Unit-cell length c length_c	88.961 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	90.00 °
Unit-cell angle γ angle_gamma	120.00 °
Molecules per unit cell Z z_pdb	6

Space group space_group	P 65
Space-group number int_tables_number	170
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	28.800 Å
R factor r_factor	0.2190
R_work r_work	0.2150
R_free r_free	0.2790

fit	/app/data/saxs_computation/z6/5z6r/5z6r.fit
pddf	/app/data/pr_computation/z6/5z6r/5z6r.pr.out
profile	/app/data/saxs_computation/z6/5z6r/5z6r.dat

SPASTIN AAA WITH ATP

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

Spastin

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