Research workbench
Crystal structure of FGF receptor 2 (FGFR2) kinase domain harboring the pathogenic K659N mutation responsible for an unclassified craniosynostosis 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
- 2PVY
- Type
- protein
- Length
- 1,142 residues
- Chains
- 4
- 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, SO4
- Pockets
- 19 · best druggability 0.73
Structure
x-ray diffraction · 4 distinct chains · 39% helix, 17% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 288 | 40% helix, 18% strand | P21802 |
| B | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 286 | 40% helix, 15% strand | P21802 |
| C | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 285 | 39% helix, 16% strand | P21802 |
| D | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 283 | 39% helix, 18% strand | P21802 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, B, D, C
- SO4 · Sulfate ion · ion · 4 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
19 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 619 | 0.73 | 0.80 | 73 | ACP |
| 2 | 467 | 0.68 | 0.79 | 52 | ACP |
| 3 | 695 | 0.65 | 0.74 | 53 | SO4 |
| 4 | 424 | 0.61 | 0.76 | 44 | empty |
| 5 | 172 | 0.57 | 0.81 | 28 | ACP |
Interfaces
4 interfaces between chains.
- A–C · 1477 Ų buried · 22 hydrogen bonds · protein-protein
- B–D · 1375 Ų buried · 19 hydrogen bonds · protein-protein
- A–D · 838 Ų buried · 11 hydrogen bonds · protein-protein
- B–C · 812 Ų buried · 12 hydrogen bonds · protein-protein
Compared structures
- 2PVY · Crystal Structure of FGF Receptor 2 (FGFR2) Kinase Domain Harboring the Pathogenic K659N… · the same entry in another collection · chain D against D, 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 D against A, TM-score 0.98
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 2PVY · PDBe 2PVY · UniProt P21802
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