Research workbench
Crystal structure of FGF receptor 2 (FGFR2) kinase domain harboring the pathogenic E565G mutation responsible for pfeiffer syndrome
Analyse Crystal structure of FGF receptor 2 (FGFR2) kinase domain harboring the… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PY3
- Type
- protein
- Length
- 566 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibroblast growth factor receptor 2
- EC
- 2.7.10.1
- UniProt
- P21802
- Ligands
- ACP, MG, SO4
- Pockets
- 4 · best druggability 0.74
Structure
x-ray diffraction · 2 distinct chains · 40% helix, 16% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 282 | 40% helix, 16% strand | P21802 |
| B | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 284 | 39% helix, 15% strand | P21802 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 2 copies · chains A, B
- MG · Magnesium ion · metal · 4 copies · chains A, B
- SO4 · Sulfate ion · ion · 4 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1067 | 0.74 | 0.77 | 77 | MG, ACP |
| 2 | 330 | 0.55 | 0.75 | 34 | SO4 |
| 3 | 70 | 0.32 | 0.75 | 18 | empty |
| 4 | 61 | 0.32 | 0.75 | 11 | empty |
Interfaces
1 interface between chains.
- A–B · 1120 Ų buried · 20 hydrogen bonds · protein-protein
Compared structures
- 2PY3 · Crystal Structure of FGF Receptor 2 (FGFR2) Kinase Domain Harboring the Pathogenic E565G… · the same entry in another collection · chain A against A, TM-score 1.00
- P21802 · AlphaFold monomer V2.0 prediction for fibroblast growth factor receptor 2 (P21802) · a predicted model of the same protein · chain A against A, TM-score 0.97
Analyse
- Open in the research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides and crosslinks on the 3D structure
- Every structure of UniProt P21802
- Elsewhere: RCSB PDB 2PY3 · PDBe 2PY3 · UniProt P21802
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