Research workbench
Crystal structure of the FGFR2 D2 domain in complex with Fab 2B.1.3
Analyse Crystal structure of the FGFR2 D2 domain in complex with Fab 2B.1.3 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4WV1
- Type
- protein
- Length
- 1,072 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fibroblast growth factor receptor 2; Fab heavy chain; Fab light chain
- EC
- 2.7.10.1
- UniProt
- P21802
- Pockets
- 11 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| F, C | Fibroblast growth factor receptor 2 (EC 2.7.10.1) | protein | 98 | 12% helix, 51% strand | P21802 |
| B, E | Fab heavy chain | protein | 224 | 4% helix, 56% strand | — |
| A, D | Fab light chain | protein | 214 | 5% helix, 50% strand | — |
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 | 345 | 0.56 | 0.76 | 40 | empty |
| 2 | 321 | 0.56 | 0.76 | 36 | empty |
| 3 | 326 | 0.53 | 0.74 | 38 | empty |
| 4 | 217 | 0.48 | 0.75 | 30 | empty |
| 5 | 122 | 0.47 | 0.79 | 33 | empty |
Interfaces
11 interfaces between chains.
- B–A · 1962 Ų buried · 21 hydrogen bonds · protein-protein
- E–D · 1954 Ų buried · 21 hydrogen bonds · protein-protein
- F–E · 826 Ų buried · 15 hydrogen bonds · protein-protein
- C–B · 812 Ų buried · 15 hydrogen bonds · protein-protein
- A–D · 293 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 4WV1 · Crystal structure of the FGFR2 D2 domain in complex with Fab 2B.1.3 · 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 C against A, TM-score 0.92
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 4WV1 · PDBe 4WV1 · UniProt P21802
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