MolNFT v1 · #25375 · protein
Complex between VEGF and a receptor blocking peptide
1VPP · Protein (vascular endothelial growth factor): “Complex between VEGF and a receptor blocking peptide”. X-ray diffraction, 3 pockets (best druggability 0.49). MolNFT v1 #25375 on GenesisL1: 3D structure, binding sites and pockets in…
- PDB
- 1VPP
- Type
- protein
- Length
- 224 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Protein (vascular endothelial growth factor); Protein (peptide V108)
- UniProt
- P15692
- Pockets
- 3 · best druggability 0.49
Structure
x-ray diffraction · 4 distinct chains · 9% helix, 59% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V | Protein (vascular endothelial growth factor) | protein | 96 | 13% helix, 60% strand | P15692 |
| W | Protein (vascular endothelial growth factor) | protein | 90 | 9% helix, 67% strand | P15692 |
| X | Protein (peptide V108) | protein | 20 | 0% helix, 40% strand | — |
| Y | Protein (peptide V108) | protein | 18 | 0% helix, 39% strand | — |
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 130 | 0.49 | 0.79 | 27 | empty |
| 2 | 78 | 0.35 | 0.76 | 23 | empty |
| 3 | 58 | 0.26 | 0.72 | 18 | empty |
Interfaces
5 interfaces between chains.
- V–W · 1449 Ų buried · 9 hydrogen bonds · protein-protein
- V–X · 664 Ų buried · 20 hydrogen bonds · protein-protein
- W–Y · 541 Ų buried · 13 hydrogen bonds · protein-protein
- V–Y · 57 Ų buried · 0 hydrogen bonds · protein-protein
- W–X · 51 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 1VPP · Complex between VEGF and a receptor blocking peptide · the same entry in another collection · chain V against V, 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 0.93
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
- Elsewhere: RCSB PDB 1VPP · PDBe 1VPP · UniProt P15692
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