SAXSdb — 5fjy

▼

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

KINESIN LIGHT CHAIN 2

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 heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 161–480 Chain B； UniProt 161–480	Fragment：TPR DOMAIN WITH N-TERMINAL EXTENSION	UNKNOWN PEPTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；8% (W/V) PGA-LM 0.3 M NA-MALONATE 0.1 M NA-CACODYLATE PH 6.5	Resolution 4.00 Å R-free 0.261
2	Protein heterocomplex Heteromer Protein × 4 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 161–480	Fragment：TPR DOMAIN WITH N-TERMINAL EXTENSION	UNKNOWN PEPTIDE × 2	X-RAY DIFFRACTION X-ray crystallization conditions：pH 6.5；8% (W/V) PGA-LM 0.3 M NA-MALONATE 0.1 M NA-CACODYLATE PH 6.5	Resolution 4.00 Å R-free 0.261

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 5FJY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3ZFW Crystal structure of the TPR domain of kinesin light chain 2 in complex with a tryptophan-acidic cargo peptide Deposited 2012-12-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 218–480（263 aa） Fragment：TPR DOMAIN, RESIDUES 218-477	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.10 M MES PH 6.5, 0.2 L-PROLINE, 7% PGA	Resolution 2.90 Å R-free 0.244
3ZFW Crystal structure of the TPR domain of kinesin light chain 2 in complex with a tryptophan-acidic cargo peptide Deposited 2012-12-12	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 218–480（263 aa） Fragment：TPR DOMAIN, RESIDUES 218-477	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；0.10 M MES PH 6.5, 0.2 L-PROLINE, 7% PGA	Resolution 2.90 Å R-free 0.244
5OJF Crystal Structure of KLC2-TPR domain (fragment [A1-B6] Deposited 2017-07-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 190–484（295 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；12 % PEG 3350, 0.5 M Phos. pH 7.5 Glycerol 25 %	Resolution 3.40 Å R-free 0.264
5OJF Crystal Structure of KLC2-TPR domain (fragment [A1-B6] Deposited 2017-07-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 190–484（295 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；12 % PEG 3350, 0.5 M Phos. pH 7.5 Glycerol 25 %	Resolution 3.40 Å R-free 0.264
5OJF Crystal Structure of KLC2-TPR domain (fragment [A1-B6] Deposited 2017-07-21	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 190–484（295 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；291 K；12 % PEG 3350, 0.5 M Phos. pH 7.5 Glycerol 25 %	Resolution 3.40 Å R-free 0.264
6EJN The KLC2 TPR domain bound to the JIP3 leucine zipper domain Deposited 2017-09-22	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 191–479（289 aa） Chain B 191–479（289 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；20% PEG 3350 0.2 M NaCSN	Resolution 3.20 Å R-free 0.210
6F9I Crystal structure of KLC2 bound to the second tryptophan-acidic motif peptide from calsyntenin-1 Deposited 2017-12-14	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 191–481（291 aa） Chain B 191–481（291 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；298 K；0.893 M sodium potassium tartrate, 0.2 M NaCl, 0.1 M imidazole pH 8.0	Resolution 3.99 Å R-free 0.273

4 other PDB entries and 7 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	Q91YS4_MOUSE
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 5–324； UniProt 161–480 Author chain B； PDBConstruct 5–324； UniProt 161–480 Author chain C； PDBConstruct 5–324； UniProt 161–480

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	5fjy
Deposition date deposition_date	2015-10-14
Structure title title	Crystal structure of mouse kinesin light chain 2 (residues 161-480)
Keywords keywords	PROTEIN TRANSPORT, MOLECULAR TRANSPORT, TPR DOMAINS, AUTOINHIBITION; PROTEIN TRANSPORT
Experimental Method method	X-RAY DIFFRACTION

▼

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

Radius of gyration Rg (Guinier) rg_guinier	37.64 Å
Radius of gyration Rg (electron density) rg_electron	37.79 Å
Forward intensity I(0) i0	133839000.00
Molecular weight molecular_weight	91070.0 kDa
Excluded volume excluded_volume	113560 Å³
Envelope volume envelope_volume	164990 Å³
Hydration-shell volume shell_volume	39196 Å³
Envelope diameter envelope_diameter	135.1 Å
Shell Rg shell_rg	40.68 Å
Envelope Rg envelope_rg	37.11 Å
Shape Rg shape_rg	37.78 Å
Total Rg total_rg	38.02 Å
Total atoms total_atoms	6405
Residues n_residues	813
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	129.7 Å
Rg (real space) rg_real	37.79 Å
Rg uncertainty (real space) rg_real_error	1.67 Å
I(0) (real space) i0_real	1.3380e+08
I(0) uncertainty (real space) i0_real_error	2.3630e+06
Rg (reciprocal space) rg_reciprocal	37.70 Å
I(0) (reciprocal space) i0_reciprocal	133800000.0000
Solution quality estimate total_estimate	0.8837
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	43.2 Å
Skewness Skewness skewness	0.373
Kurtosis Kurtosis kurtosis	-0.368
Angular range angular_range	— – 0.2100 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	8723000.0000
Real-space data points n_real_points	43
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.880; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.945; Smooth: 0.897

▶

5. Crystallography and Experiment 5. Crystallography & Experiment

▶

6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	KINESIN LIGHT CHAIN 2
Molecular weight formula_weight	36371.0 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	6405

GSHMKDSLDDLFPNEDEQSPAPSPGGGDVAAQHGGYEIPALRLTLHNLVIQYASQGRYEVAVPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLSNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGENKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKVDSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASRSRK

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

Entity 2 Entity 2 polymer

Description description	UNKNOWN PEPTIDE
Molecular weight formula_weight	443.5 kDa
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	D,E,F

XXXXX

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

▼

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

Domain ID domain_id	5fjyA00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	5fjyB00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

Domain ID domain_id	5fjyC00
Class class	1 — Mainly Alpha
Architecture architecture	25 — Alpha Horseshoe
Topology topology	40 — Serine Threonine Protein Phosphatase 5, Tetratricopeptide repeat
Homologous superfamily homologous superfamily	10 — Tetratricopeptide repeat domain

▶

8. Citations (2)

▶

Unit-cell length a length_a	148.700 Å
Unit-cell length b length_b	86.280 Å
Unit-cell length c length_c	111.740 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	98.41 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	12

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	4.000 Å
Low-resolution limit resolution_low	42.880 Å
R factor r_factor	0.2343
R_work r_work	0.2328
R_free r_free	0.2611

fit	/app/data/saxs_computation/fj/5fjy/5fjy.fit
pddf	/app/data/pr_computation/fj/5fjy/5fjy.pr.out
profile	/app/data/saxs_computation/fj/5fjy/5fjy.dat

Crystal structure of mouse kinesin light chain 2 (residues 161-480)

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

KINESIN LIGHT CHAIN 2

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 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 3 domains

CATH v4.4 (3 domains)

8. Citations (2)

9. Files and Curves (10)

Files (7)

Curves (3)