Research workbench
VEGF in complex with domain 2 of the flt-1 receptor
Analyse VEGF in complex with domain 2 of the flt-1 receptor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1FLT
- Type
- protein
- Length
- 382 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor; Fms-like tyrosine kinase 1
- EC
- 2.7.10.1
- UniProt
- P15692, P17948
- Pockets
- 5 · best druggability 0.46
Structure
x-ray diffraction · 4 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V | Vascular endothelial growth factor | protein | 95 | 13% helix, 61% strand | P15692 |
| W | Vascular endothelial growth factor | protein | 98 | 12% helix, 59% strand | P15692 |
| X | Fms-like tyrosine kinase 1 (EC 2.7.10.1) | protein | 95 | 3% helix, 47% strand | P17948 |
| Y | Fms-like tyrosine kinase 1 (EC 2.7.10.1) | protein | 94 | 3% helix, 48% strand | P17948 |
Pockets
5 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 102 | 0.46 | 0.79 | 16 | empty |
| 2 | 142 | 0.45 | 0.77 | 26 | empty |
| 3 | 122 | 0.41 | 0.76 | 21 | empty |
| 4 | 91 | 0.39 | 0.77 | 20 | empty |
| 5 | 50 | 0.23 | 0.72 | 14 | empty |
Interfaces
5 interfaces between chains.
- V–W · 1375 Ų buried · 14 hydrogen bonds · protein-protein
- W–X · 618 Ų buried · 7 hydrogen bonds · protein-protein
- V–Y · 595 Ų buried · 4 hydrogen bonds · protein-protein
- V–X · 380 Ų buried · 2 hydrogen bonds · protein-protein
- W–Y · 306 Ų buried · 1 hydrogen bond · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1FLT · VEGF in complex with domain 2 of the flt-1 receptor · the same entry in another collection · chain Y against Y, TM-score 1.00
- P15692 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor a (P15692) · a predicted model of the same protein · chain V against A, TM-score 0.98
- P17948 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor receptor 1… · a predicted model of the same protein · chain Y against A, TM-score 0.96
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 P15692
- Every structure of UniProt P17948
- Elsewhere: RCSB PDB 1FLT · PDBe 1FLT · UniProt P15692 · UniProt P17948
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