SAXSdb — 4bsk

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

VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3

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	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain A； UniProt 23–229	Fragment：LIGAND-BINDING DOMAINS D1-2, RESIDUES 23-229	VASCULAR ENDOTHELIAL GROWTH FACTOR C × 2 （P49767） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；SITTING DROPS AT ROOM TEMPERATURE OVER A RESERVOIR SOLUTION OF 0.1 M BIS-TRIS BUFFER AT PH 8.5-9.5 AND 1.0-1.5 M AMMONIUM SULPHATE.	Resolution 4.20 Å R-free 0.372

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 4BSK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
4BSJ Crystal structure of VEGFR-3 extracellular domains D4-5 Deposited 2013-06-10	Different construct 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 330–553（224 aa） Fragment：EXTRACELLULAR DOMAINS 4 AND 5 (D4-5), RESIDUES 330-553	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 4	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 298 K, PHOSPHATE BUFFER 0.1 M, PH 7.5 - 8.5, PEG 400 25%.	Resolution 2.50 Å R-free 0.253
4BSJ Crystal structure of VEGFR-3 extracellular domains D4-5 Deposited 2013-06-10	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 330–553（224 aa） Fragment：EXTRACELLULAR DOMAINS 4 AND 5 (D4-5), RESIDUES 330-553	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8；298 K；VAPOUR DIFFUSION, SITTING DROP, TEMPERATURE 298 K, PHOSPHATE BUFFER 0.1 M, PH 7.5 - 8.5, PEG 400 25%.	Resolution 2.50 Å R-free 0.253

1 other PDB entries and 2 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VGFR3_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain A； PDBConstruct 1–207； UniProt 23–229

VASCULAR ENDOTHELIAL GROWTH FACTOR C

HOMO SAPIENS

UniProt P49767

State in the Current Structure

Assembly	Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Associated Components	Method and Experimental Conditions	Structure Quality
1	Other combination Heteromer Protein × 4 其他Polymer 2 PDB declaration: tetrameric（4） Consistent with protein copy count	Chain C； UniProt 103–215	Fragment：VEGF HOMOLOGY DOMAIN, RESIDUES 103-215 Mutation：YES	VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3 × 2 （P35916） 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION, SITTING DROP；pH 9；SITTING DROPS AT ROOM TEMPERATURE OVER A RESERVOIR SOLUTION OF 0.1 M BIS-TRIS BUFFER AT PH 8.5-9.5 AND 1.0-1.5 M AMMONIUM SULPHATE.	Resolution 4.20 Å R-free 0.372

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 4BSK	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
2X1W Crystal Structure of VEGF-C in Complex with Domains 2 and 3 of VEGFR2 Deposited 2010-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain A 112–215（104 aa） Fragment：VEGF HOMOLOGY DOMAIN, RESIDUES 112-215 Chain B 112–215（104 aa） Fragment：VEGF HOMOLOGY DOMAIN, RESIDUES 112-215	Mutation：YES Mutation：YES	CS CESIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.2；100 MM MES BUFFER, PH 5.0-5.6, 50 MM CSCL AND 28-32 % (W/V) JEFFAMINE 600.	Resolution 2.70 Å R-free 0.280
2X1W Crystal Structure of VEGF-C in Complex with Domains 2 and 3 of VEGFR2 Deposited 2010-01-08	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 112–215（104 aa） Fragment：VEGF HOMOLOGY DOMAIN, RESIDUES 112-215 Chain D 112–215（104 aa） Fragment：VEGF HOMOLOGY DOMAIN, RESIDUES 112-215	Mutation：YES Mutation：YES	CS CESIUM ION × 1 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 5	X-RAY DIFFRACTION X-ray crystallization conditions pH 5.2；100 MM MES BUFFER, PH 5.0-5.6, 50 MM CSCL AND 28-32 % (W/V) JEFFAMINE 600.	Resolution 2.70 Å R-free 0.280
2X1X CRYSTAL STRUCTURE OF VEGF-C IN COMPLEX WITH DOMAINS 2 AND 3 OF VEGFR2 IN A TETRAGONAL CRYSTAL FORM Deposited 2010-01-08	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Other combination Heteromer；Protein × 4 PDB declaration: tetrameric	Chain E 112–215（104 aa） Fragment：VEGF HOMOLOGY DOMAIN, RESIDUES 112-215	Mutation：YES	HG MERCURY (II) ION × 2 NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 2	X-RAY DIFFRACTION X-ray crystallization conditions pH 4.6；100 MM NA-ACETATE BUFFER, PH 4.4-4.8, 50 MM CSCL, 28-32 % (W/V) JEFFAMINE 600	Resolution 3.10 Å R-free 0.334

2 other PDB entries and 3 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VEGFC_HUMAN
Isoform	—
PDB entities	2
Chains and sequence ranges	Author chain C； PDBConstruct 3–115； UniProt 103–215

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	4bsk
Deposition date deposition_date	2013-06-10
Structure title title	Crystal structure of VEGF-C in complex with VEGFR-3 domains D1-2
Keywords keywords	;TRANSFERASE-HORMONE COMPLEX, TRANSFERASE, LYMPHANGIOGENESIS, ANGIOGENESIS, IG DOMAIN, GLYCOPROTEIN, RECEPTOR TYROSINE KINASE, DIMERIZATION ;; TRANSFERASE/HORMONE
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	29.98 Å
Radius of gyration Rg (electron density) rg_electron	31.15 Å
Forward intensity I(0) i0	13901300.00
Molecular weight molecular_weight	26685.0 kDa
Excluded volume excluded_volume	32622 Å³
Envelope volume envelope_volume	49601 Å³
Hydration-shell volume shell_volume	17076 Å³
Envelope diameter envelope_diameter	119.4 Å
Shell Rg shell_rg	30.05 Å
Envelope Rg envelope_rg	31.15 Å
Shape Rg shape_rg	31.20 Å
Total Rg total_rg	30.88 Å
Total atoms total_atoms	1876
Residues n_residues	270
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	114.1 Å
Rg (real space) rg_real	30.74 Å
Rg uncertainty (real space) rg_real_error	1.65 Å
I(0) (real space) i0_real	1.3900e+07
I(0) uncertainty (real space) i0_real_error	2.4960e+05
Rg (reciprocal space) rg_reciprocal	30.41 Å
I(0) (reciprocal space) i0_reciprocal	13900000.0000
Solution quality estimate total_estimate	0.6950
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	21.5 Å
Skewness Skewness skewness	0.770
Kurtosis Kurtosis kurtosis	-0.004
Angular range angular_range	— – 0.2650 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	1095000.0000
Real-space data points n_real_points	54
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.345; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.092; Smooth: 0.904

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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	VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3
Molecular weight formula_weight	23856.6 kDa
EC 编号 ec_number	2.7.10.1
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	A
Atom count atom_count	1876

SGYSMTPPTLNITEESHVIDTGDSLSISCRGQHPLEWAWPGAQEAPATGDKDSEDTGVVRDCEGTDARPYCKVLLLHEVHANDTGSYVCYYKYIKARIEGTTAASSYVFVRDFEQPFINKPDTLLVNRKDAMWVPCLVSIPGLNVTLRSQSSVLWPDGQEVVWDDRRGMLVSTPLLHDALYLQCETTWGDQDFLSNPFLVHITGNELADPIEGR

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	SPODOPTERA FRUGIPERDA

Entity 2 Entity 2 polymer

Description description	VASCULAR ENDOTHELIAL GROWTH FACTOR C
Molecular weight formula_weight	13594.5 kDa
Mutation mutation	YES
Source method src_method	man
Copy count entity_count	1

Polymer Polymer

Polymer type type	polypeptide(L)
Chain IDs strand_id	C

DPTEETIKFAAAHYNTEILKSIDNEWRKTQCMPREVAIDVGKEFGVATNTFFKPPCVSVYRCGGCCNSEGLQCMNTSTSYLSKTLFEITVPLSQGPKPVTISFANHTSCRCMSKLHHHHHH

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	SPODOPTERA FRUGIPERDA

Entity 3 Entity 3 branched

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	424.4 kDa
Source method src_method	man
Copy count entity_count	1

Entity 4 Entity 4 non-polymer

Description description	2-acetamido-2-deoxy-beta-D-glucopyranose
Molecular weight formula_weight	221.2 kDa
Source method src_method	man
Copy count entity_count	4

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8. Citations (1)

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Unit-cell length a length_a	166.660 Å
Unit-cell length b length_b	166.660 Å
Unit-cell length c length_c	166.660 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	24

Space group space_group	I 2 3
Space-group number int_tables_number	197
Crystal system crystal_system	—

Resolution resolution	4.201 Å
Low-resolution limit resolution_low	19.920 Å
R factor r_factor	0.3380
R_work r_work	0.3341
R_free r_free	0.3718

fit	/app/data/saxs_computation/bs/4bsk/4bsk.fit
pddf	/app/data/pr_computation/bs/4bsk/4bsk.pr.out
profile	/app/data/saxs_computation/bs/4bsk/4bsk.dat

Crystal structure of VEGF-C in complex with VEGFR-3 domains D1-2

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

VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 3

State in the Current Structure

Other States of the Same Protein in the Database

VASCULAR ENDOTHELIAL GROWTH FACTOR C

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 branched

Entity 4 Entity 4 non-polymer

8. Citations (1)

9. Files and Curves (10)

Files (7)

Curves (3)