SAXSdb — 7eob

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

Kinesin-like protein KIF1A

Mus musculus

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 1–382	Mutation：E239K	AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, Ammonium acetate, Bis-Tris	Resolution 1.76 Å R-free 0.240

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 7EOB	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1I5S CRYSTAL STRUCTURE OF THE KIF1A MOTOR DOMAIN COMPLEXED WITH MG-ADP Deposited 2001-02-28	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 1–355（355 aa） Fragment：MOTOR DOMAIN	Mutation：P202A	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；296 K；30% PEG4000, 100mM Tris-HCl pH 8.5, 200mM sodium acetate, 8% (w/v) sucrose, 4mM MgCl2, 10mM ADP, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.20 Å R-free 0.225
1I6I CRYSTAL STRUCTURE OF THE KIF1A MOTOR DOMAIN COMPLEXED WITH MG-AMPPCP Deposited 2001-03-02	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 1–355（355 aa） Fragment：MOTOR DOMAIN	Mutation：P202A	MG MAGNESIUM ION × 1 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；296 K；27% PEG4000, 100MM MES-NAOH PH 6.5, 200MM SODIUM ACETATE. 20MM AMPPCP AND 40MM MGCL2 WERE ADDED 24 HOURS BEFORE COLLECTING X-RAY DATA, VAPOR DIFFUSION, HANGING DROP, temperature 296K	Resolution 2.00 Å R-free 0.230
1IA0 KIF1A HEAD-MICROTUBULE COMPLEX STRUCTURE IN ATP-FORM Deposited 2001-03-22	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 × 3 PDB declaration: trimeric	Chain K 3–355（353 aa） Fragment：MOTOR DOMAIN	Mutation：P202A	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TXL TAXOTERE × 1 MG MAGNESIUM ION × 1 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer buf1；pH 7.4；IMIDAZOLE 50 MM, MG-ACETATE 5 MM, EGTA 1 MM, K-ACETATE 50 MM, DTT 10 MM, PACLITAXEL 10 MICRO M cryo-EM vitrification conditions PLUNGED INTO ETHANE X-ray crystallization conditions polymerization of the microtubule；pH 6.8；296 K；pH 6.8, polymerization of the microtubule, temperature 296K	Resolution 15.00 Å
1VFV Crystal Structure of the Kif1A Motor Domain Complexed With Mg-AMPPNP Deposited 2004-04-19	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 1–355（355 aa） Fragment：Motor Domain OF Kinesin-like protein KIF1A and RESIDUES 329-334 OF Kinesin heavy chain isoform 5C	Not recorded	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；297 K；PEG4000, Sodium acetate, Tris-HCl, Xylitol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K	Resolution 1.85 Å R-free 0.245
1VFW Crystal Structure of the Kif1A Motor Domain Complexed With Mg-AMPPNP Deposited 2004-04-19	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 1–355（355 aa） Fragment：Motor Domain OF Kinesin-like protein KIF1A and RESIDUES 329-334 OF Kinesin heavy chain isoform 5C	Not recorded	MG MAGNESIUM ION × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；297 K；PEG4000, SODIUM ACETATE, Tris-HCl, Xylitol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K	Resolution 2.30 Å R-free 0.244
1VFX Crystal Structure of the Kif1A Motor Domain Complexed With ADP-Mg-AlFx Deposited 2004-04-19	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 1–355（355 aa） Fragment：Motor Domain OF Kinesin-like protein KIF1A and RESIDUES 329-334 OF Kinesin heavy chain isoform 5C	Not recorded	MG MAGNESIUM ION × 1 AF3 ALUMINUM FLUORIDE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；297 K；PEG4000, Sodium acetate, Tris-HCl, Xylitol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K	Resolution 2.55 Å R-free 0.294
1VFZ Crystal Structure of the Kif1A Motor Domain Complexed With ADP-Mg-VO4 Deposited 2004-04-19	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 1–355（355 aa） Fragment：Motor Domain OF Kinesin-like protein KIF1A and RESIDUES 329-334 OF Kinesin heavy chain isoform 5C	Not recorded	VO4 VANADATE ION × 1 MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；297 K；PEG4000, Sodium acetate, Tris-HCl, Xylitol, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 297.0K	Resolution 2.24 Å R-free 0.249
2HXF KIF1A head-microtubule complex structure in amppnp-form Deposited 2006-08-03	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 × 3 PDB declaration: trimeric	Chain C 1–355（355 aa） Fragment：KIF1A HEAD DOMAIN	Mutation：P202A	MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ANP PHOSPHOAMINOPHOSPHONIC ACID-ADENYLATE ESTER × 1	ELECTRON MICROSCOPY cryo-EM buffer IMIDAZOLE；pH 7.4；IMIDAZOLE cryo-EM vitrification conditions Ethan slash	Resolution 10.00 Å
2HXH KIF1A head-microtubule complex structure in adp-form Deposited 2006-08-03	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 × 3 PDB declaration: trimeric	Chain C 1–355（355 aa） Fragment：KIF1A head domain	Mutation：P202A	MG MAGNESIUM ION × 2 GTP GUANOSINE-5'-TRIPHOSPHATE × 1 GDP GUANOSINE-5'-DIPHOSPHATE × 1 TA1 TAXOL × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	ELECTRON MICROSCOPY cryo-EM buffer imidazole；pH 7.4；imidazole cryo-EM vitrification conditions Ethan slash	Resolution 11.00 Å
2ZFI Crystal Structure of the Kif1A Motor Domain Before Mg Release Deposited 2008-01-07	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 1–355（355 aa） Fragment：KIF1A (residues 1-355), KIF5C (residues 329-334)	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 1.55 Å R-free 0.224
2ZFJ Crystal Structure of the Kif1A Motor Domain during Mg release: Mg-releasing Transition-1 Deposited 2008-01-08	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 1–355（355 aa） Fragment：KIF1A (residues 1-355), KIF5C (residues 329-334)	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.20 Å R-free 0.298
2ZFK Crystal Structure of the Kif1A Motor Domain during Mg release: Mg-releasing Transition-2 Deposited 2008-01-08	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 1–355（355 aa） Fragment：KIF1A (residues 1-355), KIF5C (residues 329-334)	Not recorded	MG MAGNESIUM ION × 1 ADP ADENOSINE-5'-DIPHOSPHATE × 1 TRS 2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 3.61 Å R-free 0.349
2ZFL Crystal Structure of the Kif1A Motor Domain during Mg release: Mg-releasing Transition-3 Deposited 2008-01-08	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 1–355（355 aa） Fragment：KIF1A (residues 1-355), KIF5C (residues 329-334)	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.70 Å R-free 0.325
2ZFM Crystal Structure of the Kif1A Motor Domain After Mg Release Deposited 2008-01-08	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 1–355（355 aa） Fragment：KIF1A (residues 1-355), KIF5C (residues 329-334)	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；293 K；pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 293.0K	Resolution 2.31 Å R-free 0.256
7EO9 Crystal structure of KIF1A Motor-Neck domain with ADP-Mg-AlFx Deposited 2021-04-21	Different mutation/modification Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–382（382 aa）	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 1 AF3 ALUMINUM FLUORIDE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；PEG 3350, Ammonium acetate, Bis-Tris	Resolution 2.57 Å R-free 0.239

15 other PDB entries and 15 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	KIF1A_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–382； UniProt 1–382

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	7eob
Deposition date deposition_date	2021-04-21
Structure title title	Crystal structure of KIF1A Motor-Neck domain E239K mutant with ADP-Mg-AlFx
Keywords keywords	kinesin, MOTOR PROTEIN; MOTOR PROTEIN
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	22.82 Å
Radius of gyration Rg (electron density) rg_electron	22.09 Å
Forward intensity I(0) i0	29387800.00
Molecular weight molecular_weight	39580.0 kDa
Excluded volume excluded_volume	48743 Å³
Envelope volume envelope_volume	59879 Å³
Hydration-shell volume shell_volume	23398 Å³
Envelope diameter envelope_diameter	91.7 Å
Shell Rg shell_rg	28.17 Å
Envelope Rg envelope_rg	22.93 Å
Shape Rg shape_rg	22.10 Å
Total Rg total_rg	22.80 Å
Total atoms total_atoms	2769
Residues n_residues	349
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	88.7 Å
Rg (real space) rg_real	22.94 Å
Rg uncertainty (real space) rg_real_error	0.87 Å
I(0) (real space) i0_real	2.9390e+07
I(0) uncertainty (real space) i0_real_error	4.5810e+05
Rg (reciprocal space) rg_reciprocal	22.91 Å
I(0) (reciprocal space) i0_reciprocal	29390000.0000
Solution quality estimate total_estimate	0.7793
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.9 Å
Skewness Skewness skewness	0.638
Kurtosis Kurtosis kurtosis	0.474
Angular range angular_range	— – 0.3500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5683000.0000
Real-space data points n_real_points	67
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.436; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.839; Smooth: 0.979

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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	Kinesin-like protein KIF1A
Molecular weight formula_weight	43972.5 kDa
Mutation mutation	E239K
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	2876

MAGASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIPQLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKPRTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTKKVSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPNKNKKKKKTDFIPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKQIRCNAIINEDPNNKLIRELKDEVTRLRDLHHHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	Mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli

Entity 2 Entity 2 non-polymer

Description description	ALUMINUM FLUORIDE
Molecular weight formula_weight	84.0 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	MAGNESIUM ION
Molecular weight formula_weight	24.3 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	ADENOSINE-5'-DIPHOSPHATE
Molecular weight formula_weight	427.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	107

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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	7eobA01
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	850 — Kinesin
Homologous superfamily homologous superfamily	10 — Kinesin motor domain

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8. Citations (1)

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Unit-cell length a length_a	41.655 Å
Unit-cell length b length_b	57.249 Å
Unit-cell length c length_c	155.041 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	4

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

Resolution resolution	1.760 Å
Low-resolution limit resolution_low	30.000 Å
R factor r_factor	—
R_work r_work	0.2150
R_free r_free	0.2400

fit	/app/data/saxs_computation/eo/7eob/7eob.fit
pddf	/app/data/pr_computation/eo/7eob/7eob.pr.out
profile	/app/data/saxs_computation/eo/7eob/7eob.dat

Crystal structure of KIF1A Motor-Neck domain E239K mutant with ADP-Mg-AlFx

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

Kinesin-like protein KIF1A

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