4cl7

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

Method: X-RAY DIFFRACTION Dmax: 104.7 Å Quality: GOOD

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

VASCULAR ENDOTHELIAL GROWTH FACTOR RECEPTOR 1

HOMO SAPIENS

UniProt P17948

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 A; UniProt 132–225 Chain C; UniProt 132–225 Fragment:DOMAIN-2, RESIDUES 132-225 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
2 Protein homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain B; UniProt 132–225 Chain D; UniProt 132–225 Fragment:DOMAIN-2, RESIDUES 132-225 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

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.

10 other PDB entries and 15 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 A; PDBConstruct 1–94; UniProt 132–225 Author chain B; PDBConstruct 1–94; UniProt 132–225 Author chain C; PDBConstruct 1–94; UniProt 132–225 Author chain D; 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.

SAXS scattering curve SAXS Profile

SAXS profile for 4cl7

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 4cl7
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2. Structure Basics 2. Structure Basics

Entry ID entry_id4cl7
Deposition date deposition_date2014-01-13
Structure title titleCrystal structure of VEGFR-1 domain 2 in presence of Cobalt
Keywords keywordsRECEPTOR, METAL-BINDING; RECEPTOR
Experimental Method methodX-RAY DIFFRACTION

3. SAXS Parameters (CRYSOL theoretical calculation) 3. SAXS Parameters (CRYSOL)

Radius of gyration Rg (Guinier) rg_guinier29.71
Radius of gyration Rg (electron density) rg_electron29.51
Forward intensity I(0) i029683000.00
Molecular weight molecular_weight43547.0 kDa
Excluded volume excluded_volume55113 ų
Envelope volume envelope_volume74628 ų
Hydration-shell volume shell_volume22961 ų
Envelope diameter envelope_diameter108.1
Shell Rg shell_rg33.71
Envelope Rg envelope_rg29.08
Shape Rg shape_rg29.45
Total Rg total_rg30.14
Total atoms total_atoms3045
Residues n_residues372
Spherical-harmonic order n_harmonics20
q range q_range— – 0.5000 −1
Data points n_points101
Shell type shell_typedirectional
Solvent electron density solvent_density0.3340 e/ų
Shell contrast contrast_shell0.0300 e/ų
CRYSOL version crysol_version4.1.3

4. P(r) Distance Distribution (GNOM inversion) 4. P(r) Analysis (GNOM)

Maximum dimension Dmax dmax104.7
Rg (real space) rg_real30.00
Rg uncertainty (real space) rg_real_error1.29
I(0) (real space) i0_real2.9680e+07
I(0) uncertainty (real space) i0_real_error4.8580e+05
Rg (reciprocal space) rg_reciprocal29.88
I(0) (reciprocal space) i0_reciprocal29680000.0000
Solution quality estimate total_estimate0.8385
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks3
Primary peak position r_peak_primary35.6
Skewness Skewness skewness0.543
Kurtosis Kurtosis kurtosis-0.155
Angular range angular_range— – 0.2650 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3510000.0000
Real-space data points n_real_points54
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.767; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.680; Smooth: 0.920

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 8 domains

SCOP 2.08 (4 domains)

Domain ID domain_idd4cl7a_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.4 — I set domains
Domain ID domain_idd4cl7b_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.4 — I set domains
Domain ID domain_idd4cl7c_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.4 — I set domains
Domain ID domain_idd4cl7d_
Class classb — All beta proteins
Fold Fold foldb.1 — Immunoglobulin-like beta-sandwich
Superfamily Superfamily superfamilyb.1.1 — Immunoglobulin
Family Family familyb.1.1.4 — I set domains

CATH v4.4 (4 domains)

Domain ID domain_id4cl7A00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4cl7B00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4cl7C00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id4cl7D00
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)