3dar

Crystal structure of D2 domain from human FGFR2

Method: X-RAY DIFFRACTION Dmax: 75.1 Å Quality: GOOD

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

Fibroblast growth factor receptor 2

Homo sapiens

UniProt P21802

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 146–249 Fragment:D2 domain, Ig-like C2-type 2, UNP residues 146-249 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;291 K;0.2 M sodium acetate, 0.1 M Tris-HCl, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K, pH 8.5 Resolution 2.20 Å R-free 0.255
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain B; UniProt 146–249 Fragment:D2 domain, Ig-like C2-type 2, UNP residues 146-249 No other associated polymer X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 8.5;291 K;0.2 M sodium acetate, 0.1 M Tris-HCl, 30% PEG 4000, VAPOR DIFFUSION, HANGING DROP, temperature 291.0K, pH 8.5 Resolution 2.20 Å R-free 0.255

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.

60 other PDB entries and 122 assemblies. Open the comparison page and filter oligomeric states

View Construct and Data Evidence
UniProt name FGFR2_HUMAN
Isoform
PDB entities 1
Chains and sequence ranges Author chain A; PDBConstruct 2–105; UniProt 146–249 Author chain B; PDBConstruct 2–105; UniProt 146–249

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 3dar

P(r) Distance Distribution P(r) Distribution

P(r) distribution for 3dar
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2. Structure Basics 2. Structure Basics

Entry ID entry_id3dar
Deposition date deposition_date2008-05-30
Structure title titleCrystal structure of D2 domain from human FGFR2
Keywords keywords;IMMUNOGLOBULIN FOLD, ATP-binding, Craniosynostosis, Disease mutation, Ectodermal dysplasia, Glycoprotein, Heparin-binding, Immunoglobulin domain, Kinase, Lacrimo-auriculo-dento-digital syndrome, Membrane, Nucleotide-binding, Phosphoprotein, Receptor, Secreted, Transferase, Transmembrane, Tyrosine-protein kinase ;; TRANSFERASE
Experimental Method methodX-RAY DIFFRACTION

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

Radius of gyration Rg (Guinier) rg_guinier20.90
Radius of gyration Rg (electron density) rg_electron20.84
Forward intensity I(0) i09039230.00
Molecular weight molecular_weight21932.0 kDa
Excluded volume excluded_volume27245 ų
Envelope volume envelope_volume32790 ų
Hydration-shell volume shell_volume14663 ų
Envelope diameter envelope_diameter74.2
Shell Rg shell_rg25.62
Envelope Rg envelope_rg21.13
Shape Rg shape_rg20.83
Total Rg total_rg21.58
Total atoms total_atoms1545
Residues n_residues198
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 dmax75.1
Rg (real space) rg_real21.17
Rg uncertainty (real space) rg_real_error0.61
I(0) (real space) i0_real9.0390e+06
I(0) uncertainty (real space) i0_real_error1.1230e+05
Rg (reciprocal space) rg_reciprocal21.12
I(0) (reciprocal space) i0_reciprocal9039000.0000
Solution quality estimate total_estimate0.7762
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary18.5
Skewness Skewness skewness0.631
Kurtosis Kurtosis kurtosis-0.175
Angular range angular_range— – 0.3800 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha3315000.0000
Real-space data points n_real_points70
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.534; Stabil: 1.000; Sysdev: 1.000; Positv: 1.000; Valcen: 0.509; Smooth: 0.975

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (2)

7. Fold Classification (SCOP + CATH) 4 domains

SCOP 2.08 (2 domains)

Domain ID domain_idd3dara_
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_idd3darb_
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 (2 domains)

Domain ID domain_id3darA01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins
Domain ID domain_id3darB01
Class class2 — Mainly Beta
Architecture architecture60 — Sandwich
Topology topology40 — Immunoglobulin-like
Homologous superfamily homologous superfamily10 — Immunoglobulins

8. Citations (1)

9. Files and Curves (10)