SAXSdb — 1i6i

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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 1–355	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

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 1I6I	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 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
1IA0 KIF1A HEAD-MICROTUBULE COMPLEX STRUCTURE IN ATP-FORM Deposited 2001-03-22	Different construct 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 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 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 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 1–382（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
7EOB Crystal structure of KIF1A Motor-Neck domain E239K mutant with ADP-Mg-AlFx Deposited 2021-04-21	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 1–382（382 aa）	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

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 1–355； UniProt 1–355

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	1i6i
Deposition date deposition_date	2001-03-02
Structure title title	CRYSTAL STRUCTURE OF THE KIF1A MOTOR DOMAIN COMPLEXED WITH MG-AMPPCP
Keywords keywords	kinesin, motor protein, catalytic core, TRANSPORT PROTEIN; TRANSPORT 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	21.71 Å
Radius of gyration Rg (electron density) rg_electron	20.57 Å
Forward intensity I(0) i0	27549200.00
Molecular weight molecular_weight	38074.0 kDa
Excluded volume excluded_volume	46847 Å³
Envelope volume envelope_volume	57132 Å³
Hydration-shell volume shell_volume	23083 Å³
Envelope diameter envelope_diameter	79.6 Å
Shell Rg shell_rg	27.59 Å
Envelope Rg envelope_rg	21.20 Å
Shape Rg shape_rg	20.59 Å
Total Rg total_rg	21.40 Å
Total atoms total_atoms	2665
Residues n_residues	333
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	77.5 Å
Rg (real space) rg_real	21.67 Å
Rg uncertainty (real space) rg_real_error	0.63 Å
I(0) (real space) i0_real	2.7550e+07
I(0) uncertainty (real space) i0_real_error	3.5440e+05
Rg (reciprocal space) rg_reciprocal	21.68 Å
I(0) (reciprocal space) i0_reciprocal	27550000.0000
Solution quality estimate total_estimate	0.8369
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	26.6 Å
Skewness Skewness skewness	0.380
Kurtosis Kurtosis kurtosis	0.001
Angular range angular_range	— – 0.3650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	5460000.0000
Real-space data points n_real_points	68
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.654; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.961; Smooth: 0.955

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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	41102.2 kDa
Mutation mutation	P202A
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	2979

MAGASVKVAVRVRPFNSREMSRDSKCIIQMSGSTTTIVNPKQPKETPKSFSFDYSYWSHTSPEDINYASQKQVYRDIGEEMLQHAFEGYNVCIFAYGQTGAGKSYTMMGKQEKDQQGIIPQLCEDLFSRINDTTNDNMSYSVEVSYMEIYCERVRDLLNPKNKGNLRVREHPLLGPYVEDLSKLAVTSYNDIQDLMDSGNKARTVAATNMNETSSRSHAVFNIIFTQKRHDAETNITTEKVSKISLVDLAGSERADSTGAKGTRLKEGANINKSLTTLGKVISALAEMDSGPNKNKKKKKTDFIPYRDSVLTWLLRENLGGNSRTAMVAALSPADINYDETLSTLRYADRAKQIRNTVSVNHHHHH

来源 Source

来源生物 organism	Mus musculus
通用名 common_name	house mouse
NCBI Class编号 ncbi_taxonomy_id	10090
宿主生物 host_organism	Escherichia coli BL21(DE3)

Entity 2 Entity 2 non-polymer

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

Entity 3 Entity 3 non-polymer

Description description	PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER
Molecular weight formula_weight	505.2 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-AMINO-2-HYDROXYMETHYL-PROPANE-1,3-DIOL
Molecular weight formula_weight	122.1 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	231

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7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (2 domains)

Domain ID domain_id	d1i6ia1
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.37.1.9 — Motor proteins

Domain ID domain_id	d1i6ia2
Class class	l — Artifacts
Fold Fold fold	l.1 — Tags
Superfamily Superfamily superfamily	l.1.1 — Tags
Family Family family	l.1.1.1 — Tags

CATH v4.4 (1 domains)

Domain ID domain_id	1i6iA00
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	41.986 Å
Unit-cell length b length_b	56.401 Å
Unit-cell length c length_c	156.123 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	2.000 Å
Low-resolution limit resolution_low	19.700 Å
R factor r_factor	0.2200
R_work r_work	0.2190
R_free r_free	0.2300

fit	/app/data/saxs_computation/i6/1i6i/1i6i.fit
pddf	/app/data/pr_computation/i6/1i6i/1i6i.pr.out
profile	/app/data/saxs_computation/i6/1i6i/1i6i.dat

CRYSTAL STRUCTURE OF THE KIF1A MOTOR DOMAIN COMPLEXED WITH MG-AMPPCP

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