SAXSdb — 9bnc

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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 1440–1496 Chain B； UniProt 1440–1496 Chain C； UniProt 1440–1496	Fragment：trimerization domain 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

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 9BNC	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
3HON Crystal Structure of Human Collagen XVIII Trimerization Domain (cubic form) Deposited 2009-06-02	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 1441–1496（56 aa） Fragment：UNP residues 1441-1496	Mutation：A1441G	No recorded non-water small molecule	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
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 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） 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
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 1–57； UniProt 1440–1496 Author chain B； PDBConstruct 1–57； UniProt 1440–1496 Author chain C； PDBConstruct 1–57； UniProt 1440–1496

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	9bnc
Deposition date deposition_date	2024-05-02
Structure title title	Collagen XVIII trimerization domain with introduced inter-chain disulfide bond, E31C-V37C
Keywords keywords	Trimer, Disulfide, Biologic scaffold, STRUCTURAL PROTEIN; STRUCTURAL 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	16.60 Å
Radius of gyration Rg (electron density) rg_electron	15.11 Å
Forward intensity I(0) i0	6926790.00
Molecular weight molecular_weight	18814.0 kDa
Excluded volume excluded_volume	23429 Å³
Envelope volume envelope_volume	26113 Å³
Hydration-shell volume shell_volume	14461 Å³
Envelope diameter envelope_diameter	49.8 Å
Shell Rg shell_rg	21.21 Å
Envelope Rg envelope_rg	15.41 Å
Shape Rg shape_rg	15.10 Å
Total Rg total_rg	16.25 Å
Total atoms total_atoms	2608
Residues n_residues	170
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	51.0 Å
Rg (real space) rg_real	16.46 Å
Rg uncertainty (real space) rg_real_error	0.23 Å
I(0) (real space) i0_real	6.9270e+06
I(0) uncertainty (real space) i0_real_error	8.2670e+04
Rg (reciprocal space) rg_reciprocal	16.48 Å
I(0) (reciprocal space) i0_reciprocal	6927000.0000
Solution quality estimate total_estimate	0.8976
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.9 Å
Skewness Skewness skewness	0.095
Kurtosis Kurtosis kurtosis	-0.442
Angular range angular_range	— – 0.4800 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1727000.0000
Real-space data points n_real_points	78
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.906; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.986; Smooth: 0.959

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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	Collagen alpha-1(XVIII) chain
Molecular weight formula_weight	6477.5 kDa
Mutation mutation	E31C, V37C
Source method src_method	man
Copy count entity_count	3

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C
Atom count atom_count	2920

GGSSGVRLWATRQAMLGQVHEVPEGWLIFVAEQCELYVRCQNGFRKVQLEARTPLPR

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 BL21(DE3)

Entity 2 Entity 2 non-polymer

Description description	SULFATE ION
Molecular weight formula_weight	96.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	DI(HYDROXYETHYL)ETHER
Molecular weight formula_weight	106.1 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	175

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8. Citations (1)

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Unit-cell length a length_a	38.360 Å
Unit-cell length b length_b	58.078 Å
Unit-cell length c length_c	67.268 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	12

Space group space_group	P 21 21 21
Space-group number int_tables_number	19
Crystal system crystal_system	—

Resolution resolution	1.400 Å
Low-resolution limit resolution_low	32.010 Å
R factor r_factor	0.1722
R_work r_work	0.1710
R_free r_free	0.1959

fit	/app/data/saxs_computation/bn/9bnc/9bnc.fit
pddf	/app/data/pr_computation/bn/9bnc/9bnc.pr.out
profile	/app/data/saxs_computation/bn/9bnc/9bnc.dat

Collagen XVIII trimerization domain with introduced inter-chain disulfide bond, E31C-V37C

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