Research workbench
Crystal structure of FGF receptor 2 (FGFR2) kinase domain harboring the gain-of-function K659T mutation.
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
- 4J99
- Type
- protein
- Length
- 1,143 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, MG, SO4
- Pockets
- 11 · best druggability 0.83
Structure
x-ray diffraction · 3 distinct chains · 38% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 280 | 39% helix, 20% strand | P21802 |
| B, C | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 291 | 38% helix, 19% strand | P21802 |
| D | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 281 | 39% helix, 20% strand | P21802 |
Ligands and binding sites
- ACP · Phosphomethylphosphonic acid adenylate ester · ligand · 4 copies · chains A, B, C, D
- MG · Magnesium ion · metal · 3 copies · chains C, D
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 903 | 0.83 | 0.85 | 84 | ACP |
| 2 | 1095 | 0.81 | 0.82 | 88 | ACP, MG |
| 3 | 236 | 0.57 | 0.79 | 32 | empty |
| 4 | 143 | 0.47 | 0.77 | 28 | empty |
| 5 | 132 | 0.44 | 0.76 | 19 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1452 Ų buried · 13 hydrogen bonds · protein-protein
- C–D · 1317 Ų buried · 10 hydrogen bonds · protein-protein
- B–C · 482 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 242 Ų buried · 3 hydrogen bonds · protein-protein
Compared structures
- 4J99 · Crystal Structure of FGF Receptor 2 (FGFR2) Kinase Domain Harboring the Gain-of-Function… · 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 0.99
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 4J99 · PDBe 4J99 · UniProt P21802
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