SAXSdb — 3hon

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

Collagen alpha-1(XVIII) chain

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 1441–1496	Fragment：UNP residues 1441-1496 Mutation：A1441G	No other associated polymer	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, HANGING DROP；pH 6.5；298 K；0.25M MgCl2, 0.1M BisTris, 18-22% (w/v) PEG 8000, pH 6.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 3.00 Å R-free 0.288

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 3HON	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1BNL ZINC DEPENDENT DIMERS OBSERVED IN CRYSTALS OF HUMAN ENDOSTATIN Deposited 1998-07-30	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 1334–1511（178 aa） Fragment：ENDOSTATIN, 20-KDA COLLAGEN XVIII C-TERMINAL GLOBULAR DOMAIN	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.90 Å R-free 0.275
1BNL ZINC DEPENDENT DIMERS OBSERVED IN CRYSTALS OF HUMAN ENDOSTATIN Deposited 1998-07-30	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 1334–1511（178 aa） Fragment：ENDOSTATIN, 20-KDA COLLAGEN XVIII C-TERMINAL GLOBULAR DOMAIN	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.90 Å R-free 0.275
1BNL ZINC DEPENDENT DIMERS OBSERVED IN CRYSTALS OF HUMAN ENDOSTATIN Deposited 1998-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain C 1334–1511（178 aa） Fragment：ENDOSTATIN, 20-KDA COLLAGEN XVIII C-TERMINAL GLOBULAR DOMAIN	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.90 Å R-free 0.275
1BNL ZINC DEPENDENT DIMERS OBSERVED IN CRYSTALS OF HUMAN ENDOSTATIN Deposited 1998-07-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 4 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain D 1334–1511（178 aa） Fragment：ENDOSTATIN, 20-KDA COLLAGEN XVIII C-TERMINAL GLOBULAR DOMAIN	Not recorded	ZN ZINC ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 2.90 Å R-free 0.275
3HSH Crystal structure of human collagen XVIII trimerization domain (Tetragonal crystal form) Deposited 2009-06-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1441–1496（56 aa） Fragment：UNP residues 1441-1496 Chain B 1441–1496（56 aa） Fragment：UNP residues 1441-1496 Chain C 1441–1496（56 aa） Fragment：UNP residues 1441-1496	Mutation：A1441G Mutation：A1441G Mutation：A1441G	SO4 SULFATE ION × 10 GOL GLYCEROL × 7	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；298 K；1.65M ammonium sulfate, 0.1M citric acid, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.224
3HSH Crystal structure of human collagen XVIII trimerization domain (Tetragonal crystal form) Deposited 2009-06-10	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain D 1441–1496（56 aa） Fragment：UNP residues 1441-1496 Chain E 1441–1496（56 aa） Fragment：UNP residues 1441-1496 Chain F 1441–1496（56 aa） Fragment：UNP residues 1441-1496	Mutation：A1441G Mutation：A1441G Mutation：A1441G	SO4 SULFATE ION × 3 GOL GLYCEROL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；298 K；1.65M ammonium sulfate, 0.1M citric acid, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.224
3HSH Crystal structure of human collagen XVIII trimerization domain (Tetragonal crystal form) Deposited 2009-06-10	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein homooligomer Homooligomer；Protein × 24 PDB declaration: 24-meric	Chain A 1441–1496（56 aa） Fragment：UNP residues 1441-1496 Chain B 1441–1496（56 aa） Fragment：UNP residues 1441-1496 Chain C 1441–1496（56 aa） Fragment：UNP residues 1441-1496 Chain D 1441–1496（56 aa） Fragment：UNP residues 1441-1496 Chain E 1441–1496（56 aa） Fragment：UNP residues 1441-1496 Chain F 1441–1496（56 aa） Fragment：UNP residues 1441-1496	Mutation：A1441G Mutation：A1441G Mutation：A1441G Mutation：A1441G Mutation：A1441G Mutation：A1441G	SO4 SULFATE ION × 52 GOL GLYCEROL × 36	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 3.5；298 K；1.65M ammonium sulfate, 0.1M citric acid, pH 3.5, VAPOR DIFFUSION, HANGING DROP, temperature 298.0K	Resolution 1.80 Å R-free 0.224
9BNB Collagen XVIII trimerization domain with introduced inter-chain disulfide bond, G(-1)C-L5C Deposited 2024-05-02	Different construct Different mutation/modification Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1440–1496（57 aa） Chain B 1440–1496（57 aa） Chain C 1440–1496（57 aa）	Mutation：;A(-1)C, L5C (authors' numbering) ; Mutation：;A(-1)C, L5C (authors' numbering) ; Mutation：;A(-1)C, L5C (authors' numbering) ;	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.1 M Bis-Tris HCl, pH 6.5, 25% (w/v) PEG 3350	Resolution 1.50 Å R-free 0.233
9BNC Collagen XVIII trimerization domain with introduced inter-chain disulfide bond, E31C-V37C Deposited 2024-05-02	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 3 PDB declaration: trimeric	Chain A 1440–1496（57 aa） Fragment：trimerization domain Chain B 1440–1496（57 aa） Fragment：trimerization domain Chain C 1440–1496（57 aa） Fragment：trimerization domain	Mutation：E31C, V37C Mutation：E31C, V37C Mutation：E31C, V37C	SO4 SULFATE ION × 1 PEG DI(HYDROXYETHYL)ETHER × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；293 K；0.2 M Lithium Sulfate, 0.1 M Tris HCl, pH 8.5, 25% (w/v) PEG3350	Resolution 1.40 Å R-free 0.196
9BND SARS-CoV-2 spike HexaPro protein in complex with T0A trimeric antagonist Deposited 2024-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1442–1496（55 aa） Fragment：residues 1442-1496 (Uniprot numbering),Peptidase M2 domain Chain C 1442–1496（55 aa） Fragment：residues 1442-1496 (Uniprot numbering),Peptidase M2 domain Chain E 1442–1496（55 aa） Fragment：residues 1442-1496 (Uniprot numbering),Peptidase M2 domain	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；1x PBS 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.19 Å
9BNE SARS-CoV-2 spike HexaPro protein in complex with T3A trimeric antagonist Deposited 2024-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1442–1496（55 aa） Chain C 1442–1496（55 aa） Chain E 1442–1496（55 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；1x PBS 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.43 Å
9BNF SARS-CoV-2 spike HexaPro protein in complex with T5A trimeric antagonist Deposited 2024-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1442–1497（56 aa） Chain C 1442–1497（56 aa） Chain E 1442–1497（56 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 33	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；1x PBS: 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.33 Å
9BNG SARS-CoV-2 spike HexaPro protein in complex with T18A trimeric antagonist Deposited 2024-05-02	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Insufficient information Heteromer；Protein × 6 PDB declaration: hexameric	Chain A 1442–1497（56 aa） Chain C 1442–1497（56 aa） Chain E 1442–1497（56 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 28	ELECTRON MICROSCOPY cryo-EM buffer pH 7.4；1x PBS 137 mM NaCl, 2.7 mM KCl, 10 mM Na2HPO4, 1.8 mM KH2PO4 cryo-EM vitrification conditions Cryogen ETHANE	Resolution 3.73 Å

8 other PDB entries and 13 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	COIA1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–56； UniProt 1441–1496

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	3hon
Deposition date deposition_date	2009-06-02
Structure title title	Crystal Structure of Human Collagen XVIII Trimerization Domain (cubic form)
Keywords keywords	;collagen triple helix, trimerization domain, collagen XVIII, multiplexin, Alternative promoter usage, Alternative splicing, Cell adhesion, Collagen, Disulfide bond, Extracellular matrix, Glycoprotein, Hydroxylation, Metal-binding, Polymorphism, Secreted, Zinc, protein binding ;; PROTEIN BINDING
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	13.25 Å
Radius of gyration Rg (electron density) rg_electron	11.88 Å
Forward intensity I(0) i0	909678.00
Molecular weight molecular_weight	6261.0 kDa
Excluded volume excluded_volume	7880 Å³
Envelope volume envelope_volume	9542 Å³
Hydration-shell volume shell_volume	7461 Å³
Envelope diameter envelope_diameter	45.0 Å
Shell Rg shell_rg	16.64 Å
Envelope Rg envelope_rg	12.71 Å
Shape Rg shape_rg	11.86 Å
Total Rg total_rg	13.27 Å
Total atoms total_atoms	443
Residues n_residues	54
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	47.3 Å
Rg (real space) rg_real	13.28 Å
Rg uncertainty (real space) rg_real_error	0.43 Å
I(0) (real space) i0_real	9.0970e+05
I(0) uncertainty (real space) i0_real_error	9.9070e+03
Rg (reciprocal space) rg_reciprocal	13.28 Å
I(0) (reciprocal space) i0_reciprocal	909700.0000
Solution quality estimate total_estimate	0.8479
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	15.0 Å
Skewness Skewness skewness	0.403
Kurtosis Kurtosis kurtosis	-0.142
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	162300.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.736; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.872; Smooth: 0.938

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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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7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

Domain ID domain_id	3honA00
Class class	3 — Alpha Beta
Architecture architecture	40 — 3-Layer(aba) Sandwich
Topology topology	1620 — YefM-like fold
Homologous superfamily homologous superfamily	70 —

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8. Citations (1)

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Unit-cell length a length_a	94.876 Å
Unit-cell length b length_b	94.876 Å
Unit-cell length c length_c	94.876 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	48

Space group space_group	I 41 3 2
Space-group number int_tables_number	214
Crystal system crystal_system	—

Resolution resolution	3.000 Å
Low-resolution limit resolution_low	38.730 Å
R factor r_factor	0.2790
R_work r_work	0.2790
R_free r_free	0.2880

Description description	Collagen alpha-1(XVIII) chain
Molecular weight formula_weight	6442.4 kDa
Mutation mutation	A1441G
Source method src_method	man
Copy count entity_count	1

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	443

Crystal Structure of Human Collagen XVIII Trimerization Domain (cubic form)

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

Collagen alpha-1(XVIII) chain

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 (1)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

7. Fold Classification (SCOP + CATH) 1 domains

CATH v4.4 (1 domains)

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)

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

fit	/app/data/saxs_computation/ho/3hon/3hon.fit
pddf	/app/data/pr_computation/ho/3hon/3hon.pr.out
profile	/app/data/saxs_computation/ho/3hon/3hon.dat