MolNFT v1 · #53955 · protein
Structural insights into the binding of VEGF-B by vegfr-1D2: recognition and specificity
2XAC · Vascular endothelial growth factor B: “Structural insights into the binding of VEGF-B by vegfr-1D2: recognition and specificity”. X-ray diffraction, 6 pockets (best druggability 0.71). MolNFT v1 #53955 on GenesisL1: 3D structure…
- PDB
- 2XAC
- Type
- protein
- Length
- 388 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor B; Vascular endothelial growth factor receptor 1
- EC
- 2.7.10.1
- UniProt
- P49765, P17948
- Pockets
- 6 · best druggability 0.71
Structure
x-ray diffraction · 4 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Vascular endothelial growth factor B | protein | 99 | 5% helix, 58% strand | P49765 |
| B | Vascular endothelial growth factor B | protein | 97 | 6% helix, 51% strand | P49765 |
| C | Vascular endothelial growth factor receptor 1 (EC 2.7.10.1) | protein | 97 | 3% helix, 35% strand | P17948 |
| X | Vascular endothelial growth factor receptor 1 (EC 2.7.10.1) | protein | 95 | 0% helix, 45% strand | P17948 |
Ligands and binding sites
- GOL · Glycerol · additive · chains B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 120 | 0.71 | 0.92 | 28 | empty |
| 2 | 141 | 0.61 | 0.85 | 23 | empty |
| 3 | 56 | 0.41 | 0.81 | 11 | empty |
| 4 | 78 | 0.32 | 0.74 | 20 | empty |
| 5 | 76 | 0.31 | 0.73 | 18 | empty |
Interfaces
5 interfaces between chains.
- A–B · 1476 Ų buried · 19 hydrogen bonds · protein-protein
- B–X · 651 Ų buried · 2 hydrogen bonds · protein-protein
- A–C · 487 Ų buried · 2 hydrogen bonds · protein-protein
- A–X · 304 Ų buried · 1 hydrogen bond · protein-protein
- B–C · 178 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 10 disulfide (disulfide).
Compared structures
- 2XAC · Structural Insights into the Binding of VEGF-B by VEGFR-1D2: Recognition and Specificity · the same entry in another collection · chain A against A, TM-score 1.00
- P17948 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor receptor 1… · a predicted model of the same protein · chain X against A, TM-score 0.95
- P49765 · AlphaFold monomer V2.0 prediction for vascular endothelial growth factor B (P49765) · a predicted model of the same protein · chain B against A, TM-score 0.90
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 P49765
- Every structure of UniProt P17948
- Elsewhere: RCSB PDB 2XAC · PDBe 2XAC · UniProt P49765 · UniProt P17948
GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.