MolNFT v1 · #168424 · protein
Crystal structure of the Fab portion of dupilumab
6WGB · Dupilumab Fab heavy chain: “Crystal structure of the Fab portion of dupilumab”. X-ray diffraction, 4 pockets (best druggability 0.70). MolNFT v1 #168424 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6WGB
- Type
- protein
- Length
- 829 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Dupilumab Fab heavy chain; Dupilumab Fab light chain
- Pockets
- 4 · best druggability 0.70
Structure
x-ray diffraction · 4 distinct chains · 6% helix, 50% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Dupilumab Fab heavy chain | protein | 208 | 7% helix, 51% strand | — |
| B | Dupilumab Fab light chain | protein | 215 | 6% helix, 51% strand | — |
| C | Dupilumab Fab heavy chain | protein | 198 | 6% helix, 49% strand | — |
| D | Dupilumab Fab light chain | protein | 208 | 6% helix, 48% strand | — |
Pockets
4 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1088 | 0.70 | 0.75 | 120 | empty |
| 2 | 608 | 0.63 | 0.74 | 57 | empty |
| 3 | 52 | 0.36 | 0.79 | 16 | empty |
| 4 | 74 | 0.30 | 0.73 | 26 | empty |
Interfaces
4 interfaces between chains.
- A–B · 1675 Ų buried · 21 hydrogen bonds · protein-protein
- C–D · 1506 Ų buried · 16 hydrogen bonds · protein-protein
- A–D · 98 Ų buried · 0 hydrogen bonds · protein-protein
- A–C · 92 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 6WGB · Crystal structure of the fab portion of dupilumab · the same entry in another collection · chain A against A, 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
- Elsewhere: RCSB PDB 6WGB · PDBe 6WGB
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