Research workbench
Crystal structure of VEGF-a in complex with vegfr-1 domains D1-6
Analyse Crystal structure of VEGF-a in complex with vegfr-1 domains D1-6 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T89
- Type
- protein
- Length
- 1,385 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor a; Vascular endothelial growth factor receptor 1
- EC
- 2.7.10.1
- UniProt
- P15692, P17948
- Ligands
- NAG
- Pockets
- 14 · best druggability 0.74
Structure
x-ray diffraction · 3 distinct chains · 3% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V, W | Vascular endothelial growth factor a | protein | 96 | 13% helix, 60% strand | P15692 |
| X | Vascular endothelial growth factor receptor 1 (EC 2.7.10.1) | protein | 596 | 3% helix, 46% strand | P17948 |
| Y | Vascular endothelial growth factor receptor 1 (EC 2.7.10.1) | protein | 597 | 2% helix, 47% strand | P17948 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 23 copies · chains X, Y, V, W
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 817 | 0.74 | 0.78 | 58 | empty |
| 2 | 159 | 0.63 | 0.85 | 29 | empty |
| 3 | 91 | 0.53 | 0.84 | 16 | empty |
| 4 | 150 | 0.52 | 0.79 | 28 | empty |
| 5 | 212 | 0.52 | 0.77 | 29 | empty |
Interfaces
6 interfaces between chains.
- V–W · 1419 Ų buried · 14 hydrogen bonds · protein-protein
- X–Y · 1148 Ų buried · 14 hydrogen bonds · protein-protein
- V–X · 887 Ų buried · 2 hydrogen bonds · protein-protein
- W–Y · 840 Ų buried · 3 hydrogen bonds · protein-protein
- W–X · 802 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 20 glycan, 18 disulfide (N-glycosylation, disulfide, glycosylation).
Compared structures
- 5T89 · Crystal structure of VEGF-A in complex with VEGFR-1 domains D1-6 · the same entry in another collection · chain V against V, 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 Y against A, TM-score 0.81
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 5T89 · PDBe 5T89 · UniProt P15692 · UniProt P17948
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