SAXSdb — 9vx3

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

HisMab-1VH(S112C),Serine/threonine-protein kinase 4 18kDa subunit

Homo sapiens

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 × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 432–480 Chain B； UniProt 432–480	Mutation：S37C	Polyhistidine peptide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；16% (w/v) polyethylene glycol 3350, 0.1M HEPES (pH 7.0), 0.2M MgCl2	Resolution 2.39 Å R-free 0.237
2	Protein heterocomplex Heteromer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain D； UniProt 432–480 Chain E； UniProt 432–480	Mutation：S37C	Polyhistidine peptide × 1	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；293 K；16% (w/v) polyethylene glycol 3350, 0.1M HEPES (pH 7.0), 0.2M MgCl2	Resolution 2.39 Å R-free 0.237

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 9VX3	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2JO8 Solution structure of C-terminal domain of human mammalian sterile 20-like kinase 1 (MST1) Deposited 2007-02-26	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 432–480（49 aa） Fragment：C-terminal SARAH domain, database residues 432-480 Chain B 432–480（49 aa） Fragment：C-terminal SARAH domain, database residues 432-480	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；298 K；Ionic strength (raw mmCIF value) 125；Pressure AMBIENT NMR sample composition 1 mM [U-13C; U-15N] c-terminal domain of Mammalian sterile 20-like kinase 1, 100 mM sodium chloride, 2 mM DTT, 25 mM HEPES, 90% H2O/10% D2O \| 90% H2O/10% D2O	Resolution not provided
3COM Crystal structure of Mst1 kinase Deposited 2008-03-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 2–311（310 aa） Fragment：Protein kinase domain: Residues 2-311	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；294 K；1700mM Ammonium sulfate, 300mM Lithium sulfate, 100mM CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.20 Å R-free 0.244
3COM Crystal structure of Mst1 kinase Deposited 2008-03-28	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 2–311（310 aa） Fragment：Protein kinase domain: Residues 2-311	Non-standard monomer：Yes (specific site not provided by mmCIF)	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 10.5；294 K；1700mM Ammonium sulfate, 300mM Lithium sulfate, 100mM CAPS pH 10.5, VAPOR DIFFUSION, SITTING DROP, temperature 294K	Resolution 2.20 Å R-free 0.244
4NR2 Crystal structure of STK4 (MST1) SARAH domain Deposited 2013-11-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 432–480（49 aa） Fragment：SARAH domain, UNP residues 432-480 Chain B 432–480（49 aa） Fragment：SARAH domain, UNP residues 432-480	Not recorded	EDO 1,2-ETHANEDIOL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；277.15 K；2.3M sodium formate, 0.1M acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 2.00 Å R-free 0.240
4NR2 Crystal structure of STK4 (MST1) SARAH domain Deposited 2013-11-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain C 432–480（49 aa） Fragment：SARAH domain, UNP residues 432-480 Chain D 432–480（49 aa） Fragment：SARAH domain, UNP residues 432-480	Not recorded	EDO 1,2-ETHANEDIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；277.15 K；2.3M sodium formate, 0.1M acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 2.00 Å R-free 0.240
4NR2 Crystal structure of STK4 (MST1) SARAH domain Deposited 2013-11-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain E 432–480（49 aa） Fragment：SARAH domain, UNP residues 432-480 Chain F 432–480（49 aa） Fragment：SARAH domain, UNP residues 432-480	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；277.15 K；2.3M sodium formate, 0.1M acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 2.00 Å R-free 0.240
4NR2 Crystal structure of STK4 (MST1) SARAH domain Deposited 2013-11-26	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain G 432–480（49 aa） Fragment：SARAH domain, UNP residues 432-480 Chain H 432–480（49 aa） Fragment：SARAH domain, UNP residues 432-480	Not recorded	EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 4.5；277.15 K；2.3M sodium formate, 0.1M acetate pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 277.15K	Resolution 2.00 Å R-free 0.240
4OH8 Crystal Structure of the human MST1-RASSF5 SARAH heterodimer Deposited 2014-01-17	Different construct Different mutation/modification Different oligomeric state Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 432–480（49 aa） Fragment：MST1 SARAH domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.8；293 K；35% (v/v) 2-methyl-2,4-pentanediol (MPD) acetate, pH 4.8, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.28 Å R-free 0.278
6YAT Crystal structure of STK4 (MST1) in complex with compound 6 Deposited 2020-03-13	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 1–311（311 aa） Chain B 1–311（311 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	3FX (2R)-3-(cyclohexylamino)-2-hydroxypropane-1-sulfonic acid × 1 GOL GLYCEROL × 7 OJ5 4-[5-(3-chlorophenyl)-7~{H}-pyrrolo[2,3-d]pyrimidin-4-yl]morpholine × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 11；293.15 K；0.6 M ammonium sulfate, 0.1 M lithium sulfate and 0.1 M CAPS, pH 11.0	Resolution 2.58 Å R-free 0.259
8A5J Crystal structure of Human STE20-like kinase 1, MST1 in complex with compound XMU-MP-1 Deposited 2022-06-15	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 28–309（282 aa） Chain B 28–309（282 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	5BS 4-[(5,10-dimethyl-6-oxo-6,10-dihydro-5H-pyrimido[5,4-b]thieno[3,2-e][1,4]diazepin-2-yl)amino]benzenesulfonamide × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2M Ammonium citrate pH 7.0, 18% PEG3350	Resolution 2.12 Å R-free 0.248
8PAV Crystal structure of MST1 with a MAP4K1 SMOL inhibitor Deposited 2023-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–311（311 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	XOZ 1-[3,5-bis(fluoranyl)-4-[[3-(1,3-thiazol-5-yl)-1~{H}-pyrrolo[2,3-b]pyridin-4-yl]oxy]phenyl]-3-(2-methoxyethyl)urea × 1 GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；1.4 M NH4SO4, 0.3 M LiSO4, 0.1 M CAPS pH 9.8	Resolution 1.90 Å R-free 0.212
8PAV Crystal structure of MST1 with a MAP4K1 SMOL inhibitor Deposited 2023-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–311（311 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	XOZ 1-[3,5-bis(fluoranyl)-4-[[3-(1,3-thiazol-5-yl)-1~{H}-pyrrolo[2,3-b]pyridin-4-yl]oxy]phenyl]-3-(2-methoxyethyl)urea × 1 GOL GLYCEROL × 1 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；1.4 M NH4SO4, 0.3 M LiSO4, 0.1 M CAPS pH 9.8	Resolution 1.90 Å R-free 0.212
8PAW Crystal structure of MST1 with a MAP4K1 SMOL inhibitor Deposited 2023-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 1–311（311 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	ASP ASPARTIC ACID × 1 XQL 1-[3,5-bis(fluoranyl)-4-[[3-(1-propan-2-ylpyrazol-3-yl)-1~{H}-pyrrolo[2,3-b]pyridin-4-yl]oxy]phenyl]-3-(2-methoxyethyl)urea × 1 GOL GLYCEROL × 1 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；1.4 M NH4SO4, 0.3 M LiSO4, 0.1 M CAPS pH 9.8	Resolution 2.14 Å R-free 0.226
8PAW Crystal structure of MST1 with a MAP4K1 SMOL inhibitor Deposited 2023-06-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain B 1–311（311 aa）	Non-standard monomer：Yes (specific site not provided by mmCIF)	XQL 1-[3,5-bis(fluoranyl)-4-[[3-(1-propan-2-ylpyrazol-3-yl)-1~{H}-pyrrolo[2,3-b]pyridin-4-yl]oxy]phenyl]-3-(2-methoxyethyl)urea × 1 GOL GLYCEROL × 1 CXS 3-CYCLOHEXYL-1-PROPYLSULFONIC ACID × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；295 K；1.4 M NH4SO4, 0.3 M LiSO4, 0.1 M CAPS pH 9.8	Resolution 2.14 Å R-free 0.226
9IIC Crystal structure of HOIP RING2-LDD in complex with STK4 KD domain Deposited 2024-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain B 11–311（301 aa） Fragment：KD domain	Mutation：K59R	GOL GLYCEROL × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Ammonium citrate tribasic (pH 7.0), 20% w/v Polyethylene glycol 3350	Resolution 2.78 Å R-free 0.280
9IIC Crystal structure of HOIP RING2-LDD in complex with STK4 KD domain Deposited 2024-06-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 2 PDB declaration: dimeric	Chain A 11–311（301 aa） Fragment：KD domain	Mutation：K59R	GOL GLYCEROL × 1 ZN ZINC ION × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；289 K；0.2 M Ammonium citrate tribasic (pH 7.0), 20% w/v Polyethylene glycol 3350	Resolution 2.78 Å R-free 0.280

9 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	STK4_HUMAN
Isoform	—
PDB entities	1, 2
Chains and sequence ranges	Author chain A； PDBConstruct 122–170； UniProt 432–480 Author chain D； PDBConstruct 122–170； UniProt 432–480 Author chain B； PDBConstruct 119–167； UniProt 432–480 Author chain E； PDBConstruct 119–167； UniProt 432–480

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.

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2. Structure Basics 2. Structure Basics

Entry ID entry_id	9vx3
Deposition date deposition_date	2025-07-18
Structure title title	Crystal structure of the peptide-bound form of HisMab-1 Fv-clasp
Keywords keywords	HisMab-1, Fv-clasp, His-tag, IMMUNE SYSTEM; IMMUNE SYSTEM
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	31.65 Å
Radius of gyration Rg (electron density) rg_electron	30.85 Å
Forward intensity I(0) i0	92913600.00
Molecular weight molecular_weight	74296.0 kDa
Excluded volume excluded_volume	92266 Å³
Envelope volume envelope_volume	120940 Å³
Hydration-shell volume shell_volume	34162 Å³
Envelope diameter envelope_diameter	101.6 Å
Shell Rg shell_rg	36.65 Å
Envelope Rg envelope_rg	30.11 Å
Shape Rg shape_rg	30.90 Å
Total Rg total_rg	31.24 Å
Total atoms total_atoms	5218
Residues n_residues	637
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	102.1 Å
Rg (real space) rg_real	31.69 Å
Rg uncertainty (real space) rg_real_error	1.12 Å
I(0) (real space) i0_real	9.2910e+07
I(0) uncertainty (real space) i0_real_error	1.5640e+06
Rg (reciprocal space) rg_reciprocal	31.68 Å
I(0) (reciprocal space) i0_reciprocal	92910000.0000
Solution quality estimate total_estimate	0.9007
Solution quality rating solution_quality	EXCELLENT a EXCELLENT solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	34.7 Å
Skewness Skewness skewness	0.301
Kurtosis Kurtosis kurtosis	-0.617
Angular range angular_range	— – 0.2500 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	11840000.0000
Real-space data points n_real_points	51
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.932; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.968; Smooth: 0.939

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (4)

Entity 1 Entity 1 polymer

Description description	HisMab-1VH(S112C),Serine/threonine-protein kinase 4 18kDa subunit
Molecular weight formula_weight	19744.1 kDa
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,D
Atom count atom_count	5230

GREVQLQQFGAELVKPGASVKISCKASGYTFTDYNMDWVKQSHGKSLEWIGDINPNYDSTVYNQKFKGKATLTVDKSSSTAYMELRSLTSEDTAIYYCARDGAYAMDHWGQGTSVTVCSGSDYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQSKRQPILDAIEAKGTLLG

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	Homo sapiens

Entity 2 Entity 2 polymer

Description description	HisMab-1VL,Serine/threonine-protein kinase 4 18kDa subunit
Molecular weight formula_weight	18680.1 kDa
Mutation mutation	S37C
Source method src_method	man
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	B,E

GRDIVMTQSPSSLSVSAGEKVTMSCKSSQSLLNSGHQKNYLAWYQQKPGQPPKLLISGASTRESGVPDRFTGSGSGTDFTLTISSVQAEDLAVYYCQNDHRYPLTFGAGTKLELKRGSDYEFLKSWTVEDLQKRLLALDPMMEQEIEEIRQKYQCKRQPILDAIEAK

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	Homo sapiens

Entity 3 Entity 3 polymer

Description description	Polyhistidine peptide
Molecular weight formula_weight	846.9 kDa
Source method src_method	syn
Copy count entity_count	2

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C,F

HHHHHH

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	12

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8. Citations (1)

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Unit-cell length a length_a	54.139 Å
Unit-cell length b length_b	69.512 Å
Unit-cell length c length_c	93.396 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	93.78 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	4

Space group space_group	P 1 21 1
Space-group number int_tables_number	4
Crystal system crystal_system	monoclinic

Resolution resolution	2.390 Å
Low-resolution limit resolution_low	39.570 Å
R factor r_factor	0.1976
R_work r_work	0.1956
R_free r_free	0.2370

fit	/app/data/saxs_computation/vx/9vx3/9vx3.fit
pddf	/app/data/pr_computation/vx/9vx3/9vx3.pr.out
profile	/app/data/saxs_computation/vx/9vx3/9vx3.dat

Crystal structure of the peptide-bound form of HisMab-1 Fv-clasp

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

HisMab-1VH(S112C),Serine/threonine-protein kinase 4 18kDa subunit

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 (4)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 polymer

Polymer Polymer

来源 Source

Entity 3 Entity 3 polymer

Polymer Polymer

Entity 4 Entity 4 water

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)