MolNFT v1 · #109016 · protein
Vascular endothelial growth factor in complex with ALPHA/BETA-VEGF-1
4WPB · Vascular endothelial growth factor a: “Vascular endothelial growth factor in complex with ALPHA/BETA-VEGF-1”. X-ray diffraction, 1 ligand (NH2), 1 pocket (best druggability 0.50). MolNFT v1 #109016 on GenesisL1: 3D structure…
- PDB
- 4WPB
- Type
- protein
- Length
- 252 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor a; ALPHA/BETA-VEGF-1
- UniProt
- P15692
- Ligands
- NH2
- Pockets
- 1 · best druggability 0.50
Structure
x-ray diffraction · 3 distinct chains · 20% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor a | protein | 95 | 13% helix, 56% strand | P15692 |
| B | Vascular endothelial growth factor a | protein | 93 | 13% helix, 61% strand | P15692 |
| C, D | ALPHA/BETA-VEGF-1 | protein | 32 | 66% helix, 0% strand | — |
Ligands and binding sites
- NH2 · Amino group · ion · 2 copies · chains A, C, D
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 122 | 0.50 | 0.80 | 29 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1176 Ų buried · 11 hydrogen bonds · protein-protein
- B–D · 504 Ų buried · 5 hydrogen bonds · protein-protein
- A–C · 475 Ų buried · 4 hydrogen bonds · protein-protein
- B–C · 286 Ų buried · 3 hydrogen bonds · protein-protein
- A–D · 232 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 modified, 10 disulfide (nonstandard, disulfide).
Compared structures
- 4WPB · Vascular endothelial growth factor in complex with alpha/beta-VEGF-1 · the same entry in another collection · chain A against A, TM-score 1.00
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 4WPB · PDBe 4WPB · UniProt P15692
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