SAXSdb — 8dpx

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

Tumor necrosis factor receptor superfamily member 10B

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 homooligomer Homooligomer Protein × 3 PDB declaration: trimeric（3） Consistent with protein copy count	Chain A； UniProt 77–184 Chain B； UniProt 77–184 Chain C； UniProt 77–184	Not recorded	No other associated polymer	SOLUTION NMR NMR measurement conditions：pH 7.2；310 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition：400 uM [U-100% 15N, U-100% 13C, U-85% 2H] DR5 ectodomain, 4.4 mM DGS-NTA (Ni), 44 mM DMPC, 88 mM D7PC, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：500 uM [U-100% 15N; U-100% 2H] DR5 ectodomain, 5.5 mM DGS-NTA (Ni), 55 mM DMPC, 110 mM D7PC, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：250 uM [U-100% 15N; U-100% 2H] Isotopically mixed DR5 ectodomain, 250 uM [U-100% 13C] DR5 ectodomain, 5.5 mM DGS-NTA (Ni), 55 mM DMPC, 110 mM D7PC, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：250 uM [U-100% 13C; U-100% 15N; U-95% 2H] Isotopically mixed DR5 ectodomain, 250 uM DR5 ectodomain, 5.5 mM DGS-NTA (Ni), 55 mM DMPC, 110 mM D7PC, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：500 uM [U-100% 13C; U-100% 15N] DR5 ectodomain, 5.5 mM DGS-NTA (Ni), 55 mM DMPC, 110 mM D7PC, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition：400 uM [U-100% 15N, U-85% 2H] DR5 ectodomain, 4.4 mM DGS-NTA (Ni), 44 mM DMPC, 88 mM D7PC, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided

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 8DPX	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1D0G CRYSTAL STRUCTURE OF DEATH RECEPTOR 5 (DR5) BOUND TO APO2L/TRAIL Deposited 1999-09-09	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain R 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN RESIDUES 1-130 Chain S 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN RESIDUES 1-130 Chain T 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN RESIDUES 1-130	Not recorded	ZN ZINC ION × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；292 K；15% Peg8K, 10% ethylene glycol, 0.2M ammonium sulface, 0.1M Tris-HCl, pH 7.5, VAPOR DIFFUSION, HANGING DROP, temperature 19K	Resolution 2.40 Å R-free 0.267
1DU3 Crystal structure of TRAIL-SDR5 Deposited 2000-01-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN Chain B 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN Chain C 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.6；295 K；PEG 1000, Sodium Acetate, Sodium Chloride, pH 4.6, EVAPORATION, temperature 22K	Resolution 2.20 Å R-free 0.291
1DU3 Crystal structure of TRAIL-SDR5 Deposited 2000-01-14	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 6 PDB declaration: hexameric	Chain G 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN Chain H 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN Chain I 54–183（130 aa） Fragment：EXTRACELLULAR DOMAIN	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions EVAPORATION；pH 4.6；295 K；PEG 1000, Sodium Acetate, Sodium Chloride, pH 4.6, EVAPORATION, temperature 22K	Resolution 2.20 Å R-free 0.291
1ZA3 The crystal structure of the YSd1 Fab bound to DR5 Deposited 2005-04-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 54–183（130 aa） Fragment：Extra-cellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；292 K；20% PEG 8000, 0.2M MgAcetate, 0.1M NaCacodylate pH 6.2-6.6, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.35 Å R-free 0.280
1ZA3 The crystal structure of the YSd1 Fab bound to DR5 Deposited 2005-04-05	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 54–183（130 aa） Fragment：Extra-cellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.4；292 K；20% PEG 8000, 0.2M MgAcetate, 0.1M NaCacodylate pH 6.2-6.6, pH 6.4, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.35 Å R-free 0.280
2H9G Crystal structure of phage derived Fab BdF1 with human Death Receptor 5 (DR5) Deposited 2006-06-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain R 54–183（130 aa） Fragment：extra cellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；Crystals from drops containing an equal volume of protein and well solution consisting of 20% PEG 3350, 0.2M Na2HPO4, 0.1 M Bis-Tris, pH 6.1-6.8. The crystals were cryo-protected with well solution supplemented with 20% PEG 200., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.32 Å R-free 0.282
2H9G Crystal structure of phage derived Fab BdF1 with human Death Receptor 5 (DR5) Deposited 2006-06-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 54–183（130 aa） Fragment：extra cellular domain	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 6.5；292 K；Crystals from drops containing an equal volume of protein and well solution consisting of 20% PEG 3350, 0.2M Na2HPO4, 0.1 M Bis-Tris, pH 6.1-6.8. The crystals were cryo-protected with well solution supplemented with 20% PEG 200., pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 2.32 Å R-free 0.282
3X3F TRAIL-R2 Extracellular Region Complexed to a Fab fragment from Human Agonist Antibody KMTR2 Deposited 2015-01-20	Different construct Different mutation/modification 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 A 54–184（131 aa） Fragment：UNP residues 54-184	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CL CHLORIDE ION × 1 GOL GLYCEROL × 5	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7.5；293 K；7.5% PEG 3350, 75mM calcium chloride, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 2.10 Å R-free 0.224
4I9X Crystal structure of human cytomegalovirus glycoprotein UL141 targeting the death receptor TRAIL-R2 Deposited 2012-12-05	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 58–184（127 aa） Fragment：TRAIL-R2, UNP residues 58-184 Chain D 58–184（127 aa） Fragment：TRAIL-R2, UNP residues 58-184	Non-standard monomer：Yes (specific site not provided by mmCIF) Non-standard monomer：Yes (specific site not provided by mmCIF)	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 1 CA CALCIUM ION × 4 NA SODIUM ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 9.5；295.15 K；20% PEG 8K, CHES, pH 9.5, VAPOR DIFFUSION, SITTING DROP, temperature 295.15K	Resolution 2.10 Å R-free 0.274
4N90 Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody Deposited 2013-10-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain T 57–182（126 aa） Fragment：UNP residues 57-182	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM Tris pH 8.0, 1.0 M LiCl, 0.2 M MnCl2, 10% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.286
4N90 Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody Deposited 2013-10-18	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain S 57–182（126 aa） Fragment：UNP residues 57-182	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM Tris pH 8.0, 1.0 M LiCl, 0.2 M MnCl2, 10% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.286
4N90 Crystal structure of ternary complex of TRAIL, DR5, and Fab fragment from a DR5 agonist antibody Deposited 2013-10-18	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain R 57–182（126 aa） Fragment：UNP residues 57-182	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；293 K；100 mM Tris pH 8.0, 1.0 M LiCl, 0.2 M MnCl2, 10% PEG6000, VAPOR DIFFUSION, HANGING DROP, temperature 293K	Resolution 3.30 Å R-free 0.286
4OD2 Crystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5 Deposited 2014-01-09	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 3 PDB declaration: trimeric	Chain S 73–183（111 aa） Fragment：UNP residues 73-183	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8；292 K；Protein (7mg/mL in 20 mM Tris-HCl, 150 mM NaCl) was mixed with equal volume of well solution (30% PEG 4K, 0.1 M Tris-HCl pH 8.5, 0.2M MgCl2), VAPOR DIFFUSION, HANGING DROP, temperature 292K	Resolution 3.20 Å R-free 0.305
6NHW Structure of the transmembrane domain of the Death Receptor 5 - Dimer of Trimer Deposited 2018-12-24	Different construct Different mutation/modification Different oligomeric state Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 6 PDB declaration: hexameric	Chain A 208–242（35 aa） Fragment：residues 208-242 Chain B 208–242（35 aa） Fragment：residues 208-242 Chain C 208–242（35 aa） Fragment：residues 208-242 Chain D 208–242（35 aa） Fragment：residues 208-242 Chain E 208–242（35 aa） Fragment：residues 208-242 Chain F 208–242（35 aa） Fragment：residues 208-242	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.8 mM [U-13C; U-15N; 85%-2H] Transmembrane Domain of Death Receptor 5, 50 mM DMPC, 100 mM DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.8 mM [U-13C; U-15N] Transmembrane Domain of Death Receptor 5, 50 mM [acyl chain U-2H] DMPC, 100 mM [acyl chain U-2H] DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.4 mM [U-15N; U-2H; 15%-13C] Transmembrane Domain of Death Receptor 5, 50 mM [acyl chain U-2H] DMPC, 100 mM [acyl chain U-2H] DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6NHY Structure of the transmembrane domain of the Death Receptor 5 mutant (G217Y) - Trimer Only Deposited 2018-12-24	Different construct Different mutation/modification Different experimental conditions	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 208–242（35 aa） Chain B 208–242（35 aa） Chain C 208–242（35 aa）	Mutation：G217Y Mutation：G217Y Mutation：G217Y	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 7；303 K；Ionic strength (raw mmCIF value) 50；Pressure 1 NMR sample composition 0.8 mM [U-13C; U-15N; 85%-2H] Transmembrane Domain of DR5 Mutant G217Y, 50 mM DMPC, 100 mM DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.8 mM [U-13C; U-15N] Transmembrane Domain of DR5 Mutant G217Y, 50 mM [acyl chain U-2H] DMPC, 100 mM [acyl chain U-2H] DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O NMR sample composition 0.4 mM [15%-13C; U-15N; H-2H] Transmembrane Domain of DR5 Mutant G217Y, 50 mM [acyl chain U-2H] DMPC, 100 mM [acyl chain U-2H] DHPC, 20 mM sodium phosphate, 95% H2O/5% D2O \| 95% H2O/5% D2O	Resolution not provided
6T3J Dual Epitope Targeting by Anti-DR5 Antibodies Deposited 2019-10-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain E 58–184（127 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；281 K；10% (w/v) PEG 4000 200 mM ammonium sulphate 100 mM Sodium acetate pH 4.6	Resolution 3.05 Å R-free 0.282
6T3J Dual Epitope Targeting by Anti-DR5 Antibodies Deposited 2019-10-11	Different construct Different mutation/modification Different oligomeric state Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 5 PDB declaration: pentameric	Chain J 58–184（127 aa）	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 4.6；281 K；10% (w/v) PEG 4000 200 mM ammonium sulphate 100 mM Sodium acetate pH 4.6	Resolution 3.05 Å R-free 0.282

11 other PDB entries and 17 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	TR10B_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–108； UniProt 77–184 Author chain B； PDBConstruct 1–108； UniProt 77–184 Author chain C； PDBConstruct 1–108； UniProt 77–184

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	8dpx
Deposition date deposition_date	2022-07-17
Structure title title	Preligand association structure of DR5
Keywords keywords	preligand association structure, autoinhibition state, APOPTOSIS; APOPTOSIS
Experimental Method method	SOLUTION NMR

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

Radius of gyration Rg (Guinier) rg_guinier	28.55 Å
Radius of gyration Rg (electron density) rg_electron	28.97 Å
Forward intensity I(0) i0	5471640000.00
Molecular weight molecular_weight	547900.0 kDa
Excluded volume excluded_volume	651500 Å³
Envelope volume envelope_volume	89238 Å³
Hydration-shell volume shell_volume	26360 Å³
Envelope diameter envelope_diameter	123.7 Å
Shell Rg shell_rg	34.22 Å
Envelope Rg envelope_rg	32.00 Å
Shape Rg shape_rg	28.99 Å
Total Rg total_rg	28.98 Å
Total atoms total_atoms	72135
Residues n_residues	4905
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	113.5 Å
Rg (real space) rg_real	28.86 Å
Rg uncertainty (real space) rg_real_error	1.39 Å
I(0) (real space) i0_real	5.4720e+09
I(0) uncertainty (real space) i0_real_error	8.9490e+07
Rg (reciprocal space) rg_reciprocal	28.77 Å
I(0) (reciprocal space) i0_reciprocal	5471000000.0000
Solution quality estimate total_estimate	0.7897
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	1
Primary peak position r_peak_primary	30.4 Å
Skewness Skewness skewness	0.470
Kurtosis Kurtosis kurtosis	-0.186
Angular range angular_range	— – 0.2800 Å⁻¹
Current regularization parameter α current_alpha	0.0002
Highest regularization parameter α highest_alpha	1067000.0000
Real-space data points n_real_points	57
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.628; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.380; Smooth: 0.997

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (1)

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8. Citations (1)

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Description description	Tumor necrosis factor receptor superfamily member 10B
Molecular weight formula_weight	12232.6 kDa
Source method src_method	man
Copy count entity_count	3

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	72135

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	Komagataella pastoris

fit	/app/data/saxs_computation/dp/8dpx/8dpx.fit
pddf	/app/data/pr_computation/dp/8dpx/8dpx.pr.out
profile	/app/data/saxs_computation/dp/8dpx/8dpx.dat

Preligand association structure of DR5

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

Tumor necrosis factor receptor superfamily member 10B

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

6. Entities and Polymers Entities & Polymers (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)