SAXSdb — 6ysy

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

Myosin-4

OrganismNot specified

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 1–1938	Non-standard monomer：Yes (specific site not provided by mmCIF)	Myosin light chain 1/3, skeletal muscle isoform × 1 （P02602） ADP ADENOSINE-5'-DIPHOSPHATE × 1 VO4 VANADATE ION × 1 MG MAGNESIUM ION × 1 PJT (9~{S})-5-methyl-12-(4-morpholin-4-ylphenyl)-9-oxidanyl-4-thia-2,12-diazatricyclo[7.3.0.0^{3,7}]dodeca-1,3(7),5-trien-8-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；35% PEG600, 20mM DTT; 100mM HEPES pH 7.0; 5% DMSO	Resolution 3.25 Å R-free 0.232

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.

No other PDB entry for the same UniProt protein was found.

View Construct and Data Evidence

UniProt name	MYH4_RABIT
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–1938； UniProt 1–1938

Myosin light chain 1/3, skeletal muscle isoform

OrganismNot specified

UniProt P02602

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 B； UniProt 1–192	Not recorded	Myosin-4 × 1 （Q28641） ADP ADENOSINE-5'-DIPHOSPHATE × 1 VO4 VANADATE ION × 1 MG MAGNESIUM ION × 1 PJT (9~{S})-5-methyl-12-(4-morpholin-4-ylphenyl)-9-oxidanyl-4-thia-2,12-diazatricyclo[7.3.0.0^{3,7}]dodeca-1,3(7),5-trien-8-one × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；291 K；35% PEG600, 20mM DTT; 100mM HEPES pH 7.0; 5% DMSO	Resolution 3.25 Å R-free 0.232

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 6YSY	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
5H53 The structure of rabbit skeletal muscle actomyosin rigor complex at 5.2 angstrom. Deposited 2016-11-04	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain C 41–192（152 aa） Fragment：UNP residues 41-192	Not recorded	ADP ADENOSINE-5'-DIPHOSPHATE × 2	ELECTRON MICROSCOPY cryo-EM buffer pH 7.5 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 5.20 Å

1 other PDB entries and 1 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	MYL1_RABIT
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain B； PDBConstruct 1–192； UniProt 1–192

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	6ysy
Deposition date deposition_date	2020-04-23
Structure title title	Skeletal Myosin bound to MPH-220, MgADP-VO4
Keywords keywords	myofibril, muscle spasticity, actin binding, inhibitor, 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	35.69 Å
Radius of gyration Rg (electron density) rg_electron	35.68 Å
Forward intensity I(0) i0	170322000.00
Molecular weight molecular_weight	105810.0 kDa
Excluded volume excluded_volume	132780 Å³
Envelope volume envelope_volume	176040 Å³
Hydration-shell volume shell_volume	43377 Å³
Envelope diameter envelope_diameter	142.5 Å
Shell Rg shell_rg	39.74 Å
Envelope Rg envelope_rg	36.32 Å
Shape Rg shape_rg	35.66 Å
Total Rg total_rg	36.03 Å
Total atoms total_atoms	7437
Residues n_residues	921
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	133.0 Å
Rg (real space) rg_real	36.01 Å
Rg uncertainty (real space) rg_real_error	1.34 Å
I(0) (real space) i0_real	1.7030e+08
I(0) uncertainty (real space) i0_real_error	3.2220e+06
Rg (reciprocal space) rg_reciprocal	35.81 Å
I(0) (reciprocal space) i0_reciprocal	170300000.0000
Solution quality estimate total_estimate	0.8052
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	36.3 Å
Skewness Skewness skewness	0.619
Kurtosis Kurtosis kurtosis	0.046
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0001
Highest regularization parameter α highest_alpha	26680000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.602; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.714; Smooth: 0.942

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (7)

Entity 1 Entity 1 polymer

Description description	Myosin-4
Molecular weight formula_weight	223485.0 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	7474

MRKDADMAIFGEAAPYLRKSEKERIEAQNKPFDAKSSVFVADPKESFVKATVQSREGGKVTAKTEAGATVTVKEDQVFPMNPPKYDKIEDMAMMTHLHEPAVLYNLKERYAAWMIYTYSGLFCVTVNPYKWLPVYNAEVVTAYRGKKRQEAPPHIFSISDNAYQFMLTDRENQSILITGESGAGKTVNTKRVIQYFATIAVTGDKKKEEATSGKMQGTLEDQIISANPLLEAFANAKTVRNDNSSRFGKFIRIHFGTTGKLASADIETYLLEKSRVTFQLKAERSYHIFYQIMSNKKPDLIEMLLITTNPYDYAFVSQGEITVPSIDDQEELMATDSAIDILGFTSDERVSIYKLTGAVMHYGNMKFKQKQREEQAEPDGTEVADKAAYLQSLNSXDLLKALCYPRVKVGNEYVTKGQTVQQVYNSVGALAKAVYEKMFLWMVTRINQQLDTKQPRQYFIGVLDIAGFEIFDFNSLEQLCINFTNEKLQQFFNHHMFVLEQEEYKKEGIEWTFIDFGMDLAACIELIEKPMGIFSILEEECMFPKATDTSFKNKLYEQHLGKSNNFQKPKPAKRKVEAHFSLVHYAGTVDYNITGWLDKNKDPLNETVVGLYQKSAMKTLAFLFTGTAAAEAEGGGKKGGKKKGSSFQTVSALFRENLNKLMTNLRSTHPHFVRCIIPNETKTPGAMEHELVLHQLRCNGVLEGIRICRKGFPSRILYADFKQRYKVLNASAIPEGQFIDSKKASEKLLGSIDVDHTQYKFGHTKVFFKAGLLGLLEEMRDDKLAQLITRTQAMCRGFLARVEYKKMVERRESIFCIQYNIRAFMNVKHWPWMKLYFKIKPLLKSAETEKEMANMKEEFEKTKESLAKAEAKEKELEEKMVALMQEKNDLQLQVQAEADSLADAEERCDQLIKTKIQLEAKIKEVTERAEDEEEINAELTAKKRKLEDECSELKKDIDDLELTLAKVEKEKHATENKVKNLTEEMAGLDETIAKLTKEKKALQEAHQQTLDDLQAEEDKVNTLTKAKTKLEQQVDDLEGSLEQEKKIRMDLERAKRKLEGDLKLAQESTMDIENDKQQLDEKLKKKEFEMSNLQSKIEDEQALAMQLQKKIKELQARIEELEEEIEAERASRAKAEKQRSDLSRELEEISERLEEAGGATSAQIEMNKKREAEFQKMRRDLEEATLQHEATAATLRKKHADSVAELGEQIDNLQRVKQKLEKEKSELKMEIDDLASNMETVSKAKGNLEKMCRTLEDQVSELKTKEEEHQRLINDLSAQRARLQTESGEFSRQLDEKDSLVSQLSRGKQAFTQQIEELKRQLEEEIKAKSALAHALQSARHDCDLLREQYEEEQEAKAELQRAMSKANSEVAQWRTKYETDAIQRTEELEEAKKKLAQRLQDAEEHVEAVNAKCASLEKTKQRLQNEVEDLMIDVERTNAACAALDKKQRNFDKILAEWKHKYEETHAELEASQKESRSLSTEVFKVKNAYEESLDQLETLKRENKNLQQEISDLTEQIAEGGKRIHELEKVKKQVEQEKSELQAALEEAEASLEHEEGKILRIQLELNQVKSEIDRKIAEKDEEIDQLKRNHIRVVESMQSTLDAEIRSRNDAIRIKKKMEGDLNEMEIQLNHANRMAAEALRNYRNTQGILKDTQLHLDDALRGQEDLKEQLAMVERRANLLQAEIEELRATLEQTERSRKVAEQELLDASERVQLLHTQNTSLINTKKKLETDISQIQGEMEDIVQEARNAEEKAKKAITDAAMMAEELKKEQDTSAHLERMKKNMEQTVKDLQHRLDEAEQLALKGGKKQIQKLEARVRELEAEVESEQKRNVEAVKGLRKHERRVKELTYQTEEDRKNVLRLQDLVDKLQAKVKSYKRQAEEAEEQCNINLSKFRKLQHELEEAEERADIAESQVNKLRVKSREVHTKVISEE

Entity 2 Entity 2 polymer

Description description	Myosin light chain 1/3, skeletal muscle isoform
Molecular weight formula_weight	20974.8 kDa
Source method src_method	nat
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B

MAPKKDVKKPAAAAAPAPAPAPAPAPAPAKPKEEKIDLSAIKIEFSKEQQDEFKEAFLLYDRTGDSKITLSQVGDVLRALGTNPTNAEVKKVLGNPSNEEMNAKKIEFEQFLPMLQAISNNKDQGTYEDFVEGLRVFDKEGNGTVMGAELRHVLATLGEKMKEEEVEALMAGQEDSNGCINYEAFVKHIMSI

Entity 3 Entity 3 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 4 Entity 4 non-polymer

Description description	VANADATE ION
Molecular weight formula_weight	114.9 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 5 Entity 5 non-polymer

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

Entity 6 Entity 6 non-polymer

Description description	(9~{S})-5-methyl-12-(4-morpholin-4-ylphenyl)-9-oxidanyl-4-thia-2,12-diazatricyclo[7.3.0.0^{3,7}]dodeca-1,3(7),5-trien-8-one
Molecular weight formula_weight	383.5 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 7 Entity 7 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	32

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8. Citations (1)

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Unit-cell length a length_a	49.607 Å
Unit-cell length b length_b	119.424 Å
Unit-cell length c length_c	176.631 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	3.246 Å
Low-resolution limit resolution_low	98.930 Å
R factor r_factor	0.2183
R_work r_work	0.2175
R_free r_free	0.2323

fit	/app/data/saxs_computation/ys/6ysy/6ysy.fit
pddf	/app/data/pr_computation/ys/6ysy/6ysy.pr.out
profile	/app/data/saxs_computation/ys/6ysy/6ysy.dat

Skeletal Myosin bound to MPH-220, MgADP-VO4

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

Myosin-4

State in the Current Structure

Other States of the Same Protein in the Database

Myosin light chain 1/3, skeletal muscle isoform

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 (7)

Entity 1 Entity 1 polymer

Polymer Polymer

Entity 2 Entity 2 polymer

Polymer Polymer

Entity 3 Entity 3 non-polymer

Entity 4 Entity 4 non-polymer

Entity 5 Entity 5 non-polymer

Entity 6 Entity 6 non-polymer

Entity 7 Entity 7 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)