Research workbench
Dual specific BH1 Fab in complex with VEGF
Analyse Dual specific BH1 Fab in complex with VEGF in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BDY
- Type
- protein
- Length
- 528 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment -heavy chain; Fab fragment -light chain; Vascular endothelial growth factor a
- UniProt
- P15692
- Pockets
- 4 · best druggability 0.62
Structure
x-ray diffraction · 3 distinct chains · 7% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab fragment -heavy chain | protein | 216 | 7% helix, 53% strand | — |
| L | Fab fragment -light chain | protein | 217 | 6% helix, 52% strand | — |
| V | Vascular endothelial growth factor a | protein | 95 | 12% helix, 62% strand | P15692 |
Ligands and binding sites
- GOL · Glycerol · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 631 | 0.62 | 0.74 | 65 | empty |
| 2 | 53 | 0.45 | 0.84 | 19 | empty |
| 3 | 153 | 0.41 | 0.74 | 31 | empty |
| 4 | 110 | 0.38 | 0.74 | 23 | GOL |
Interfaces
3 interfaces between chains.
- H–L · 1657 Ų buried · 13 hydrogen bonds · protein-protein
- L–V · 517 Ų buried · 12 hydrogen bonds · protein-protein
- H–V · 302 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 7 disulfide (disulfide).
Compared structures
- 3BDY · Dual specific bH1 Fab in complex with VEGF · the same entry in another collection · chain H against H, 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 3BDY · PDBe 3BDY · UniProt P15692
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