SAXSdb — 1bnl

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

COLLAGEN XVIII

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 monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain A； UniProt 1334–1511	Fragment：ENDOSTATIN, 20-KDA COLLAGEN XVIII C-TERMINAL GLOBULAR DOMAIN	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
2	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain B； UniProt 1334–1511	Fragment：ENDOSTATIN, 20-KDA COLLAGEN XVIII C-TERMINAL GLOBULAR DOMAIN	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
3	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain C； UniProt 1334–1511	Fragment：ENDOSTATIN, 20-KDA COLLAGEN XVIII C-TERMINAL GLOBULAR DOMAIN	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
4	Protein monomer Monomer Protein × 1 PDB declaration: monomeric（1） Consistent with protein copy count	Chain D； UniProt 1334–1511	Fragment：ENDOSTATIN, 20-KDA COLLAGEN XVIII C-TERMINAL GLOBULAR DOMAIN	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

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 1BNL	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
3HON Crystal Structure of Human Collagen XVIII Trimerization Domain (cubic form) Deposited 2009-06-02	Different construct Different mutation/modification Different oligomeric state 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 oligomeric state 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 oligomeric state 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 oligomeric state 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
9BNC Collagen XVIII trimerization domain with introduced inter-chain disulfide bond, E31C-V37C Deposited 2024-05-02	Different construct Different mutation/modification Different oligomeric state 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 10 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 1–178； UniProt 1334–1511 Author chain B； PDBConstruct 1–178； UniProt 1334–1511 Author chain C； PDBConstruct 1–178； UniProt 1334–1511 Author chain D； PDBConstruct 1–178； UniProt 1334–1511

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	1bnl
Deposition date deposition_date	1998-07-30
Structure title title	ZINC DEPENDENT DIMERS OBSERVED IN CRYSTALS OF HUMAN ENDOSTATIN
Keywords keywords	ENDOSTATIN, COLLAGEN XVIII, COLLAGEN, ANTIANGIOGENIC, ANGIOGENIC, ANGIOGENISIS, CANCER, ZINC, EXTRACELLULAR MATRIX; EXTRACELLULAR MATRIX
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	36.30 Å
Radius of gyration Rg (electron density) rg_electron	35.28 Å
Forward intensity I(0) i0	100288000.00
Molecular weight molecular_weight	78523.0 kDa
Excluded volume excluded_volume	97435 Å³
Envelope volume envelope_volume	130320 Å³
Hydration-shell volume shell_volume	30903 Å³
Envelope diameter envelope_diameter	108.6 Å
Shell Rg shell_rg	41.91 Å
Envelope Rg envelope_rg	33.91 Å
Shape Rg shape_rg	35.27 Å
Total Rg total_rg	35.78 Å
Total atoms total_atoms	5532
Residues n_residues	712
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	109.8 Å
Rg (real space) rg_real	36.17 Å
Rg uncertainty (real space) rg_real_error	0.79 Å
I(0) (real space) i0_real	1.0030e+08
I(0) uncertainty (real space) i0_real_error	1.4830e+06
Rg (reciprocal space) rg_reciprocal	36.26 Å
I(0) (reciprocal space) i0_reciprocal	100300000.0000
Solution quality estimate total_estimate	0.7953
Solution quality rating solution_quality	GOOD a GOOD solution
P(r) peaks n_peaks	3
Primary peak position r_peak_primary	54.9 Å
Skewness Skewness skewness	-0.039
Kurtosis Kurtosis kurtosis	-0.896
Angular range angular_range	— – 0.2200 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	17200000.0000
Real-space data points n_real_points	45
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.795; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.949; Smooth: 0.000

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5. Crystallography and Experiment 5. Crystallography & Experiment

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6. Entities and Polymers Entities & Polymers (2)

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7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_id	d1bnla_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.5 — Endostatin

Domain ID domain_id	d1bnlb_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.5 — Endostatin

Domain ID domain_id	d1bnlc_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.5 — Endostatin

Domain ID domain_id	d1bnld_
Class class	d — Alpha and beta proteins (a+b)
Fold Fold fold	d.169 — C-type lectin-like
Superfamily Superfamily superfamily	d.169.1 — C-type lectin-like
Family Family family	d.169.1.5 — Endostatin

CATH v4.4 (4 domains)

Domain ID domain_id	1bnlA00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1bnlB00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1bnlC00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

Domain ID domain_id	1bnlD00
Class class	3 — Alpha Beta
Architecture architecture	10 — Roll
Topology topology	100 — Mannose-Binding Protein A; Chain A
Homologous superfamily homologous superfamily	10 — Mannose-Binding Protein A, subunit A

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8. Citations (1)

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Unit-cell length a length_a	92.713 Å
Unit-cell length b length_b	74.266 Å
Unit-cell length c length_c	137.805 Å
Unit-cell angle α angle_alpha	90.00 °
Unit-cell angle β angle_beta	102.55 °
Unit-cell angle γ angle_gamma	90.00 °
Molecules per unit cell Z z_pdb	16

Space group space_group	C 1 2 1
Space-group number int_tables_number	5
Crystal system crystal_system	—

Resolution resolution	2.900 Å
Low-resolution limit resolution_low	10.000 Å
R factor r_factor	0.2400
R_work r_work	0.2400
R_free r_free	0.2750

Description description	COLLAGEN XVIII
Molecular weight formula_weight	19587.2 kDa
Source method src_method	man
Copy count entity_count	4

Polymer type type	polypeptide(L)
Chain IDs strand_id	A,B,C,D
Atom count atom_count	5532

ZINC DEPENDENT DIMERS OBSERVED IN CRYSTALS OF HUMAN ENDOSTATIN

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

COLLAGEN XVIII

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 (2)

Entity 1 Entity 1 polymer

Polymer Polymer

来源 Source

Entity 2 Entity 2 non-polymer

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

CATH v4.4 (4 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	NS/0 MURINE MYELOMA CELLS

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	4

fit	/app/data/saxs_computation/bn/1bnl/1bnl.fit
pddf	/app/data/pr_computation/bn/1bnl/1bnl.pr.out
profile	/app/data/saxs_computation/bn/1bnl/1bnl.dat