SAXSdb — 4ckv

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

VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1

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 × 2 PDB declaration: dimeric（2） Consistent with protein copy count	Chain X； UniProt 132–225	Fragment：DOMAIN-2, RESIDUES 132-225	ZN ZINC ION × 2 EDO 1,2-ETHANEDIOL × 8	X-RAY DIFFRACTION X-ray crystallization conditions：VAPOR DIFFUSION；pH 7.5；291 K；VAPOR DIFFUSION METHOD, MOTHER LIQUOR:1MM VEGFR-1-D2,0.1%(W/V) DDM,4MM LAXAPHYCINE-A,5MM HEPES/NAOH PH 7.5. RESERVOIR:18% (W/V) PEG8000,100MM HEPES/NAOH PH 7.5, 18C	Resolution 2.06 Å R-free 0.205

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 4CKV	Assembly / Oligomeric State	Construct	Mutations and Modifications	Ligands, Ions and Non-polymers	Method and Experimental Conditions	Structure Quality
1FLT VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1997-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain X 132–226（95 aa） Fragment：SECOND EXTRACELLULAR IGG LIKE DOMAIN, RESIDUES 129 - 229 Chain Y 132–226（95 aa） Fragment：SECOND EXTRACELLULAR IGG LIKE DOMAIN, RESIDUES 129 - 229	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.70 Å R-free 0.261
1FLT VEGF IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1997-11-20	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain X 132–226（95 aa） Fragment：SECOND EXTRACELLULAR IGG LIKE DOMAIN, RESIDUES 129 - 229 Chain Y 132–226（95 aa） Fragment：SECOND EXTRACELLULAR IGG LIKE DOMAIN, RESIDUES 129 - 229	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions pH 8.5；pH 8.5	Resolution 1.70 Å R-free 0.261
1QSV THE VEGF-BINDING DOMAIN OF FLT-1, 20 NMR STRUCTURES Deposited 1999-06-23	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 129–229（101 aa） Fragment：SECOND EXTRACELLULAR IMMUNOGLOBULIN-LIKE DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.7；300 K；Ionic strength (raw mmCIF value) 150mM；Pressure AMBIENT NMR sample composition 1MM FLT-1(DOMAIN2) U-15N,13C; PHOSPHATE BUFFERED SALINE, PH 5.7; 50UM EDTA; 100UM NAN3; 50UM DSS NMR sample composition 1MM FLT-1(DOMAIN2) U-15N; PHOSPHATE BUFFERED SALINE, PH 5.7; 50UM EDTA; 100UM NAN3; 50UM DSS	Resolution not provided
1QSZ THE VEGF-BINDING DOMAIN OF FLT-1 (MINIMIZED MEAN) Deposited 1999-06-24	Different construct Different oligomeric state Different ligand/ion Different experimental method Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain A 129–229（101 aa） Fragment：SECOND EXTRACELLULAR IMMUNOGLOBULIN-LIKE DOMAIN	Not recorded	No recorded non-water small molecule	SOLUTION NMR NMR measurement conditions pH 5.7；300 K；Ionic strength (raw mmCIF value) 150mM；Pressure AMBIENT NMR sample composition 1MM FLT-1(DOMAIN2) U-15N,13C; PHOSPHATE BUFFERED SALINE, PH 5.7; 50UM EDTA; 100UM NAN3; 50UM DSS NMR sample composition 1MM FLT-1(DOMAIN2) U-15N; PHOSPHATE BUFFERED SALINE, PH 5.7; 50UM EDTA; 100UM NAN3; 50UM DSS NMR sample composition 1MM FLT-1(DOMAIN2) 15% 13C; PHOSPHATE BUFFERED SALINE, PH 5.7; 50UM EDTA; 100UM NAN3; 50UM DSS	Resolution not provided
1QTY VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1999-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain X 129–229（101 aa） Fragment：DOMAIN 2 Chain Y 129–229（101 aa） Fragment：DOMAIN 2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.284
1QTY VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1999-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain T 129–229（101 aa） Fragment：DOMAIN 2 Chain U 129–229（101 aa） Fragment：DOMAIN 2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.284
1QTY VASCULAR ENDOTHELIAL GROWTH FACTOR IN COMPLEX WITH DOMAIN 2 OF THE FLT-1 RECEPTOR Deposited 1999-06-29	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein heterocomplex Heteromer；Protein × 8 PDB declaration: octameric	Chain T 129–229（101 aa） Fragment：DOMAIN 2 Chain U 129–229（101 aa） Fragment：DOMAIN 2 Chain X 129–229（101 aa） Fragment：DOMAIN 2 Chain Y 129–229（101 aa） Fragment：DOMAIN 2	Not recorded	No recorded non-water small molecule	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 8.5；277 K；PEG 4000, AMMONIUMSULFATE, TRIS , pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 277K	Resolution 2.70 Å R-free 0.284
1RV6 Crystal Structure of PlGF in Complex with Domain 2 of VEGFR1 Deposited 2003-12-12	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain X 130–229（100 aa） Fragment：domain-2 Chain Y 130–229（100 aa） Fragment：domain-2	Not recorded	B3P 2-[3-(2-HYDROXY-1,1-DIHYDROXYMETHYL-ETHYLAMINO)-PROPYLAMINO]-2-HYDROXYMETHYL-PROPANE-1,3-DIOL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 6.5；pH 6.5	Resolution 2.45 Å R-free 0.260
2XAC Structural Insights into the Binding of VEGF-B by VEGFR-1D2: Recognition and Specificity Deposited 2010-03-30	Different construct Different mutation/modification Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein heterocomplex Heteromer；Protein × 4 PDB declaration: tetrameric	Chain C 129–226（98 aa） Fragment：DOMAIN 2, RESIDUES 129-226 Chain X 129–226（98 aa） Fragment：DOMAIN 2, RESIDUES 129-226	Not recorded	GOL GLYCEROL × 1	X-RAY DIFFRACTION X-ray crystallization conditions pH 8；14% PEG 4000, 0.1M SODIUM CITRATE, PH 5.6 AND 0.2M LICL	Resolution 2.71 Å R-free 0.364
3HNG Crystal structure of VEGFR1 in complex with N-(4-Chlorophenyl)-2-((pyridin-4-ylmethyl)amino)benzamide Deposited 2009-05-31	Different construct 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 801–1158（358 aa） Fragment：KINASE DOMAIN, UNP residues 801-1158	Not recorded	8ST N-(4-chlorophenyl)-2-[(pyridin-4-ylmethyl)amino]benzamide × 1 CL CHLORIDE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, SITTING DROP；pH 8.5；277 K；0.2M potassium formate, 20% PEG 3350, pH 8.5, VAPOR DIFFUSION, SITTING DROP, temperature 277K	Resolution 2.70 Å R-free 0.260
4CL7 Crystal structure of VEGFR-1 domain 2 in presence of Cobalt Deposited 2014-01-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain A 132–225（94 aa） Fragment：DOMAIN-2, RESIDUES 132-225 Chain C 132–225（94 aa） Fragment：DOMAIN-2, RESIDUES 132-225	Not recorded	CO COBALT (II) ION × 3 EDO 1,2-ETHANEDIOL × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTAL WERE OBTAINED BY HANGING DROP METHOD FROM 1MM VEGFR1-D2, 5MM HEPES/NAOH PH7.0, 10MM COCL2, 100 MM BIS-TRIS/HCL PH6.5 15%(W/V) PEG3350.	Resolution 2.00 Å R-free 0.233
4CL7 Crystal structure of VEGFR-1 domain 2 in presence of Cobalt Deposited 2014-01-13	Different construct Different mutation/modification Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 2 Protein homooligomer Homooligomer；Protein × 2 PDB declaration: dimeric	Chain B 132–225（94 aa） Fragment：DOMAIN-2, RESIDUES 132-225 Chain D 132–225（94 aa） Fragment：DOMAIN-2, RESIDUES 132-225	Not recorded	CO COBALT (II) ION × 2 EDO 1,2-ETHANEDIOL × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION, HANGING DROP；pH 7；CRYSTAL WERE OBTAINED BY HANGING DROP METHOD FROM 1MM VEGFR1-D2, 5MM HEPES/NAOH PH7.0, 10MM COCL2, 100 MM BIS-TRIS/HCL PH6.5 15%(W/V) PEG3350.	Resolution 2.00 Å R-free 0.233
5ABD CRYSTAL STRUCTURE OF VEGFR-1 DOMAIN 2 IN PRESENCE OF CU Deposited 2015-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 1 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain E 132–226（95 aa） Fragment：DOMAIN-2, RESIDUES 132-226	Not recorded	NA SODIUM ION × 1 SO4 SULFATE ION × 1	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；VAPOR DIFFUSION METHOD, MOTHER LIQUOR: 1.5MICROM VERGFR1-D2, 15MM TRIS/HCL PH 8.1, 25MM NACL, 5MM CUSO4 RESERVOIR: 19.5% (W/V) PEG8000, 100MM SA,	Resolution 2.00 Å R-free 0.222
5ABD CRYSTAL STRUCTURE OF VEGFR-1 DOMAIN 2 IN PRESENCE OF CU Deposited 2015-08-05	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 I 132–226（95 aa） Fragment：DOMAIN-2, RESIDUES 132-226	Not recorded	CU COPPER (II) ION × 2	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；VAPOR DIFFUSION METHOD, MOTHER LIQUOR: 1.5MICROM VERGFR1-D2, 15MM TRIS/HCL PH 8.1, 25MM NACL, 5MM CUSO4 RESERVOIR: 19.5% (W/V) PEG8000, 100MM SA,	Resolution 2.00 Å R-free 0.222
5ABD CRYSTAL STRUCTURE OF VEGFR-1 DOMAIN 2 IN PRESENCE OF CU Deposited 2015-08-05	Different construct Different oligomeric state Different ligand/ion Different experimental conditions Different structure-quality metrics	Assembly 3 Protein monomer Monomer；Protein × 1 PDB declaration: monomeric	Chain X 132–226（95 aa） Fragment：DOMAIN-2, RESIDUES 132-226	Not recorded	NA SODIUM ION × 1 SO4 SULFATE ION × 1 CU COPPER (II) ION × 3	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 7.5；291 K；VAPOR DIFFUSION METHOD, MOTHER LIQUOR: 1.5MICROM VERGFR1-D2, 15MM TRIS/HCL PH 8.1, 25MM NACL, 5MM CUSO4 RESERVOIR: 19.5% (W/V) PEG8000, 100MM SA,	Resolution 2.00 Å R-free 0.222
5T89 Crystal structure of VEGF-A in complex with VEGFR-1 domains D1-6 Deposited 2016-09-07	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 X 27–656（630 aa） Chain Y 27–656（630 aa）	Not recorded	NAG 2-acetamido-2-deoxy-beta-D-glucopyranose × 19	X-RAY DIFFRACTION X-ray crystallization conditions VAPOR DIFFUSION；pH 6.5；293 K；10-14% PEG3000 200 mM calcium chloride 100 mM MES pH 6.5	Resolution 4.00 Å R-free 0.315

10 other PDB entries and 16 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence

UniProt name	VGFR1_HUMAN
Isoform	—
PDB entities	1
Chains and sequence ranges	Author chain X； PDBConstruct 1–94； UniProt 132–225

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	4ckv
Deposition date deposition_date	2014-01-09
Structure title title	Crystal structure of VEGFR-1 domain 2 in presence of Zn
Keywords keywords	RECEPTOR; RECEPTOR
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	14.52 Å
Radius of gyration Rg (electron density) rg_electron	13.07 Å
Forward intensity I(0) i0	2493720.00
Molecular weight molecular_weight	11106.0 kDa
Excluded volume excluded_volume	14054 Å³
Envelope volume envelope_volume	15850 Å³
Hydration-shell volume shell_volume	10504 Å³
Envelope diameter envelope_diameter	46.7 Å
Shell Rg shell_rg	18.55 Å
Envelope Rg envelope_rg	13.45 Å
Shape Rg shape_rg	13.03 Å
Total Rg total_rg	14.48 Å
Total atoms total_atoms	776
Residues n_residues	94
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	48.6 Å
Rg (real space) rg_real	14.46 Å
Rg uncertainty (real space) rg_real_error	0.27 Å
I(0) (real space) i0_real	2.4940e+06
I(0) uncertainty (real space) i0_real_error	2.6670e+04
Rg (reciprocal space) rg_reciprocal	14.47 Å
I(0) (reciprocal space) i0_reciprocal	2494000.0000
Solution quality estimate total_estimate	0.7050
Solution quality rating solution_quality	REASONABLE a REASONABLE solution
P(r) peaks n_peaks	2
Primary peak position r_peak_primary	17.8 Å
Skewness Skewness skewness	0.246
Kurtosis Kurtosis kurtosis	-0.214
Angular range angular_range	— – 0.5000 Å⁻¹
Current regularization parameter α current_alpha	0.0000
Highest regularization parameter α highest_alpha	478600.0000
Real-space data points n_real_points	80
GNOM version gnom_version	4.1.3
Quality Criteria quality_criteria	AN1: 0.000; Oscil: 0.801; Stabil: 1.000; Sysdev: 0.256; Positv: 1.000; Valcen: 0.998; Smooth: 0.990

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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 1
Molecular weight formula_weight	10805.6 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	X
Atom count atom_count	897

GRPFVEMYSEIPEIIHMTEGRELVIPCRVTSPNITVTLKKFPLDTLIPDGKRIIWDSRKGFIISNATYKEIGLLTCEATVNGHLYKTNYLTHRQ

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

Entity 2 Entity 2 non-polymer

Description description	ZINC ION
Molecular weight formula_weight	65.4 kDa
Source method src_method	syn
Copy count entity_count	1

Entity 3 Entity 3 non-polymer

Description description	1,2-ETHANEDIOL
Molecular weight formula_weight	62.1 kDa
Source method src_method	syn
Copy count entity_count	4

Entity 4 Entity 4 water

Description description	water
Molecular weight formula_weight	18.0 kDa
Source method src_method	nat
Copy count entity_count	81

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7. Fold Classification (SCOP + CATH) 2 domains

SCOP 2.08 (1 domains)

Domain ID domain_id	d4ckvx_
Class class	b — All beta proteins
Fold Fold fold	b.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamily	b.1.1 — Immunoglobulin
Family Family family	b.1.1.4 — I set domains

CATH v4.4 (1 domains)

Domain ID domain_id	4ckvX00
Class class	2 — Mainly Beta
Architecture architecture	60 — Sandwich
Topology topology	40 — Immunoglobulin-like
Homologous superfamily homologous superfamily	10 — Immunoglobulins

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8. Citations (1)

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Unit-cell length a length_a	95.730 Å
Unit-cell length b length_b	102.390 Å
Unit-cell length c length_c	27.470 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	8

Space group space_group	C 2 2 21
Space-group number int_tables_number	20
Crystal system crystal_system	—

Resolution resolution	2.055 Å
Low-resolution limit resolution_low	47.865 Å
R factor r_factor	0.1650
R_work r_work	0.1628
R_free r_free	0.2053

fit	/app/data/saxs_computation/ck/4ckv/4ckv.fit
pddf	/app/data/pr_computation/ck/4ckv/4ckv.pr.out
profile	/app/data/saxs_computation/ck/4ckv/4ckv.dat

Crystal structure of VEGFR-1 domain 2 in presence of Zn

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

VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1

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