3cly

Crystal Structure of FGF Receptor 2 (FGFR2) Kinase Domains Trapped in Trans-Phosphorylation Reaction

Method: X-RAY DIFFRACTION Dmax: 65.3 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 homooligomer Homooligomer Protein × 2 PDB declaration: dimeric(2) Consistent with protein copy count Chain A; UniProt 458–778 Fragment:Protein Kinase Domain Mutation:C491A Non-standard monomer:Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 4 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 2 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;100 mM HEPES pH7.5, 26% PEG 4000, 200 mM (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.00 Å R-free 0.247
2 Protein monomer Monomer Protein × 1 PDB declaration: monomeric(1) Consistent with protein copy count Chain A; UniProt 458–778 Fragment:Protein Kinase Domain Mutation:C491A Non-standard monomer:Yes (specific site not provided by mmCIF) MG MAGNESIUM ION × 2 ACP PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER × 1 X-RAY DIFFRACTION X-ray crystallization conditions:VAPOR DIFFUSION, HANGING DROP;pH 7.5;298 K;100 mM HEPES pH7.5, 26% PEG 4000, 200 mM (NH4)2SO4, VAPOR DIFFUSION, HANGING DROP, temperature 298K Resolution 2.00 Å R-free 0.247

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 14–334; UniProt 458–778

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 3cly

P(r) Distance Distribution P(r) Distribution

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

Entry ID entry_id3cly
Deposition date deposition_date2008-03-20
Structure title titleCrystal Structure of FGF Receptor 2 (FGFR2) Kinase Domains Trapped in Trans-Phosphorylation Reaction
Keywords keywords;Kinase Domain, Trans-Phosphorylation, ATP-binding, Disease mutation, Ectodermal dysplasia, Glycoprotein, Heparin-binding, Immunoglobulin domain, 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_guinier20.23
Radius of gyration Rg (electron density) rg_electron19.37
Forward intensity I(0) i019467900.00
Molecular weight molecular_weight32978.0 kDa
Excluded volume excluded_volume41112 ų
Envelope volume envelope_volume48712 ų
Hydration-shell volume shell_volume20820 ų
Envelope diameter envelope_diameter68.9
Shell Rg shell_rg26.03
Envelope Rg envelope_rg19.90
Shape Rg shape_rg19.40
Total Rg total_rg20.21
Total atoms total_atoms2303
Residues n_residues289
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 dmax65.3
Rg (real space) rg_real20.16
Rg uncertainty (real space) rg_real_error0.39
I(0) (real space) i0_real1.9470e+07
I(0) uncertainty (real space) i0_real_error2.3670e+05
Rg (reciprocal space) rg_reciprocal20.18
I(0) (reciprocal space) i0_reciprocal19470000.0000
Solution quality estimate total_estimate0.8114
Solution quality rating solution_quality GOOD a GOOD solution
P(r) peaks n_peaks2
Primary peak position r_peak_primary24.2
Skewness Skewness skewness0.276
Kurtosis Kurtosis kurtosis-0.320
Angular range angular_range— – 0.3950 −1
Current regularization parameter α current_alpha0.0000
Highest regularization parameter α highest_alpha5849000.0000
Real-space data points n_real_points71
GNOM version gnom_version4.1.3
Quality Criteria quality_criteria AN1: 0.000; Oscil: 0.849; Stabil: 0.999; Sysdev: 1.000; Positv: 1.000; Valcen: 0.998; Smooth: 0.000

5. Crystallography and Experiment 5. Crystallography & Experiment

6. Entities and Polymers Entities & Polymers (4)

7. Fold Classification (SCOP + CATH) 3 domains

SCOP 2.08 (1 domains)

Domain ID domain_idd3clya_
Class classd — Alpha and beta proteins (a+b)
Fold Fold foldd.144 — Protein kinase-like (PK-like)
Superfamily Superfamily superfamilyd.144.1 — Protein kinase-like (PK-like)
Family Family familyd.144.1.7 — Protein kinases, catalytic subunit

CATH v4.4 (2 domains)

Domain ID domain_id3clyA01
Class class3 — Alpha Beta
Architecture architecture30 — 2-Layer Sandwich
Topology topology200 — Phosphorylase Kinase; domain 1
Homologous superfamily homologous superfamily20 — Phosphorylase Kinase; domain 1
Domain ID domain_id3clyA02
Class class1 — Mainly Alpha
Architecture architecture10 — Orthogonal Bundle
Topology topology510 — Transferase(Phosphotransferase); domain 1
Homologous superfamily homologous superfamily10 — Transferase(Phosphotransferase) domain 1

8. Citations (1)

9. Files and Curves (10)