SAXSdb — 3zfw

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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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain A； UniProt 218–480	Fragment：TPR DOMAIN, RESIDUES 218-477	PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY M MEMBER 2 × 1 （Q8IWE5）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain B； UniProt 218–480	Fragment：TPR DOMAIN, RESIDUES 218-477	PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY M MEMBER 2 × 1 （Q8IWE5）	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

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 3ZFW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5FJY Crystal structure of mouse kinesin light chain 2 (residues 161-480) Deposited 2015-10-14	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 161–480（320 aa） Fragment：TPR DOMAIN WITH N-TERMINAL EXTENSION Chain B 161–480（320 aa） Fragment：TPR DOMAIN WITH N-TERMINAL EXTENSION	Not recorded	No recorded non-water small molecule	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
5FJY Crystal structure of mouse kinesin light chain 2 (residues 161-480) Deposited 2015-10-14	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 161–480（320 aa） Fragment：TPR DOMAIN WITH N-TERMINAL EXTENSION	Not recorded	No recorded non-water small molecule	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
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 mutation/modification Different oligomeric state 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 mutation/modification Different oligomeric state 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 1–263； UniProt 218–480 Author chain B； PDBConstruct 1–263； UniProt 218–480

PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY M MEMBER 2

HOMO SAPIENS

UniProt Q8IWE5

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain X； UniProt 203–212	Not recorded	KINESIN LIGHT CHAIN 2 × 1 （Q91YS4）	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
2	Protein heterocomplex Heteromer Protein × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain Y； UniProt 203–212	Not recorded	KINESIN LIGHT CHAIN 2 × 1 （Q91YS4）	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

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 3ZFW	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3CXB Crystal Structure of sifa and skip Deposited 2008-04-24	Different construct Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 773–884（112 aa） Fragment：PH motif, UNP residues 773-884	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；20% Poly acrylic acid5100, 0.05M magnesium chloride, 0.1M Hepes, pH7.5, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.60 Å R-free 0.288
3HW2 Crystal structure of the SifA-SKIP(PH) complex Deposited 2009-06-17	Different construct Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 771–875（105 aa） Fragment：Pleskrin homology (PH) domain, UNP residues 771-876	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；293 K；30% PEG 4000, 0.2M Na acetate trihydrate, 0.1 M Tris-HCl, pH 8.0, VAPOR DIFFUSION, SITTING DROP, temperature 293K	Resolution 3.30 Å R-free 0.309
8JCA Cyrstal structure of SKIP RUN domain in complex with GTP-bound Arl8b(Q75L) Deposited 2023-05-10	Different construct Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 1–165（165 aa）	Not recorded	GTP GUANOSINE-5'-TRIPHOSPHATE × 1 MG MAGNESIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；298 K；800mM Potassiam phosphate dibasic 1.2 M Sodium phosphate monobasic 0.1M CAPS/Sodium hydroxide 0.2M Lithium sulfate pH10.5	Resolution 1.65 Å R-free 0.206

3 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	PKHM2_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain X； PDBConstruct 22–31； UniProt 203–212 Author chain Y； PDBConstruct 22–31； UniProt 203–212

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	3zfw
Deposition date deposition_date	2012-12-12
Structure title title	Crystal structure of the TPR domain of kinesin light chain 2 in complex with a tryptophan-acidic cargo peptide
Keywords keywords	HYDROLASE, KINESIN-CARGO RECOGNITION, MOTOR PROTEIN, TPR DOMAIN, SALMONELLA; HYDROLASE
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	36.91 Å
Radius of gyration Rg (electron density) rg_electron	37.13 Å
Forward intensity I(0) i0	47123200.00
Molecular weight molecular_weight	53305.0 kDa
Excluded volume excluded_volume	66417 Å³
Envelope volume envelope_volume	92690 Å³
Hydration-shell volume shell_volume	24500 Å³
Envelope diameter envelope_diameter	134.1 Å
Shell Rg shell_rg	36.01 Å
Envelope Rg envelope_rg	37.15 Å
Shape Rg shape_rg	37.15 Å
Total Rg total_rg	36.99 Å
Total atoms total_atoms	3749
Residues n_residues	472
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	134.7 Å
Rg (real space) rg_real	37.66 Å
Rg uncertainty (real space) rg_real_error	2.06 Å
I(0) (real space) i0_real	4.7120e+07
I(0) uncertainty (real space) i0_real_error	9.0220e+05
Rg (reciprocal space) rg_reciprocal	37.20 Å
I(0) (reciprocal space) i0_reciprocal	47100000.0000
Solution quality estimate total_estimate	0.6948
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.585
Kurtosis Kurtosis kurtosis	-0.480
Angular range angular_range	— – 0.2150 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	2521000.0000
Real-space data points n_real_points	44
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.373; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.092; Smooth: 0.818

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

Entity 1 Entity 1 polymer

Description description	KINESIN LIGHT CHAIN 2
Molecular weight formula_weight	29861.9 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B
Atom count atom_count	3749

VPLCKQALEDLEKTSGHDHPDVATMLNILALVYRDQNKYKDAAHLLNDALAIREKTLGKDHPAVAATLNNLAVLYGKRGKYKEAEPLCKRALEIREKVLGKFHPDVAKQLSNLALLCQNQGKAEEVEYYYRRALEIYATRLGPDDPNVAKTKNNLASCYLKQGKYQDAETLYKEILTRAHEKEFGSVNGENKPIWMHAEEREESKDKRRDSAPYGEYGSWYKACKVDSPTVNTTLRSLGALYRRQGKLEAAHTLEDCASRSRK

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	PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY M MEMBER 2
Molecular weight formula_weight	4716.0 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	X,Y

MGSSHHHHHHSSGLVPRGSHMTNLEWDDSAITGSTGSTGSTGSHM

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

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7. Fold Classification (SCOP + CATH) 2 domains

CATH v4.4 (2 domains)

Domain ID domain_id	3zfwA00
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	3zfwB00
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

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8. Citations (1)

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Unit-cell length a length_a	87.810 Å
Unit-cell length b length_b	90.860 Å
Unit-cell length c length_c	94.040 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 21 21 2
Space-group number int_tables_number	18
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	52.420 Å
R factor r_factor	0.2042
R_work r_work	0.2022
R_free r_free	0.2445

fit	/app/data/saxs_computation/zf/3zfw/3zfw.fit
pddf	/app/data/pr_computation/zf/3zfw/3zfw.pr.out
profile	/app/data/saxs_computation/zf/3zfw/3zfw.dat

Crystal structure of the TPR domain of kinesin light chain 2 in complex with a tryptophan-acidic cargo peptide

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

PLECKSTRIN HOMOLOGY DOMAIN-CONTAINING FAMILY M MEMBER 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) 2 domains

CATH v4.4 (2 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)