Research workbench
Structure of the B20-4 Fab, a phage derived Fab fragment, in complex with VEGF
Analyse Structure of the B20-4 Fab, a phage derived Fab fragment, 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
- 2FJH
- Type
- protein
- Length
- 1,058 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Vascular endothelial growth factor a; Fab fragment light chain; Fab fragment heavy chain
- UniProt
- Q96NW5
- Pockets
- 9 · best druggability 0.75
Structure
x-ray diffraction · 5 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| V | Vascular endothelial growth factor a | protein | 98 | 12% helix, 58% strand | Q96NW5 |
| L | Fab fragment light chain | protein | 214 | 7% helix, 50% strand | — |
| H, B | Fab fragment heavy chain | protein | 219 | 7% helix, 51% strand | — |
| W | Vascular endothelial growth factor a | protein | 97 | 12% helix, 57% strand | Q96NW5 |
| A | Fab fragment light chain | protein | 211 | 5% helix, 50% strand | — |
Pockets
9 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1028 | 0.75 | 0.78 | 99 | empty |
| 2 | 160 | 0.63 | 0.85 | 36 | empty |
| 3 | 591 | 0.62 | 0.74 | 54 | empty |
| 4 | 484 | 0.58 | 0.73 | 53 | empty |
| 5 | 177 | 0.46 | 0.75 | 31 | empty |
Interfaces
8 interfaces between chains.
- L–H · 1777 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1714 Ų buried · 15 hydrogen bonds · protein-protein
- V–H · 554 Ų buried · 3 hydrogen bonds · protein-protein
- W–B · 519 Ų buried · 3 hydrogen bonds · protein-protein
- V–L · 372 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 disulfide (disulfide).
Compared structures
- 2FJH · Structure of the B20-4 Fab, a phage derived Fab fragment, in complex with VEGF · the same entry in another collection · chain V against V, 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 Q96NW5
- Elsewhere: RCSB PDB 2FJH · PDBe 2FJH · UniProt Q96NW5
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