Research workbench
Dual-acting Fab 5A12 in complex with VEGF
Analyse Dual-acting Fab 5A12 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
- 4ZFF
- Type
- protein
- Length
- 1,035 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fragment antigen binding (Fab) 5A12 heavy chain; Fragment antigen binding (Fab) 5A12…
- UniProt
- P15692
- Ligands
- SO4
- Pockets
- 16 · best druggability 0.63
Structure
x-ray diffraction · 6 distinct chains · 8% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fragment antigen binding (Fab) 5A12 heavy chain | protein | 206 | 6% helix, 50% strand | — |
| B | Fragment antigen binding (Fab) 5A12 light chain | protein | 210 | 7% helix, 53% strand | — |
| C | Vascular endothelial growth factor a | protein | 96 | 13% helix, 63% strand | P15692 |
| D | Vascular endothelial growth factor a | protein | 99 | 12% helix, 61% strand | P15692 |
| H | Fragment antigen binding (Fab) 5A12 heavy chain | protein | 211 | 6% helix, 53% strand | — |
| L | Fragment antigen binding (Fab) 5A12 light chain | protein | 213 | 8% helix, 53% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
16 pockets found on a 1 Å grid, 6 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 612 | 0.63 | 0.74 | 58 | empty |
| 2 | 56 | 0.59 | 0.92 | 20 | empty |
| 3 | 498 | 0.58 | 0.73 | 58 | empty |
| 4 | 178 | 0.52 | 0.78 | 24 | empty |
| 5 | 61 | 0.52 | 0.87 | 20 | empty |
Interfaces
11 interfaces between chains.
- H–L · 1860 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1838 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 1433 Ų buried · 13 hydrogen bonds · protein-protein
- C–H · 411 Ų buried · 5 hydrogen bonds · protein-protein
- A–D · 406 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide (disulfide).
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 4ZFF · PDBe 4ZFF · UniProt P15692
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