Research workbench
Crystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5
Analyse Crystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4OD2
- Type
- protein
- Length
- 520 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment of drozitumab, light chain; Fab fragment of drozitumab, heavy chain; Tumor…
- UniProt
- O14763
- Pockets
- 5 · best druggability 0.58
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Fab fragment of drozitumab, light chain | protein | 209 | 6% helix, 51% strand | — |
| B | Fab fragment of drozitumab, heavy chain | protein | 214 | 5% helix, 52% strand | — |
| S | Tumor necrosis factor receptor superfamily member 10B | protein | 97 | 0% helix, 29% strand | O14763 |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 507 | 0.58 | 0.73 | 66 | empty |
| 2 | 52 | 0.38 | 0.80 | 17 | empty |
| 3 | 59 | 0.37 | 0.79 | 13 | empty |
| 4 | 95 | 0.34 | 0.74 | 18 | empty |
| 5 | 72 | 0.32 | 0.75 | 15 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1642 Ų buried · 20 hydrogen bonds · protein-protein
- A–S · 523 Ų buried · 10 hydrogen bonds · protein-protein
- B–S · 508 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 11 disulfide (disulfide).
Compared structures
- 4OD2 · Crystal structure of the Fab fragment of an anti-DR5 antibody bound to DR5 · the same entry in another collection · chain A against A, TM-score 1.00
- O14763 · AlphaFold monomer V2.0 prediction for tumor necrosis factor receptor superfamily member… · a predicted model of the same protein · chain S against A, TM-score 0.92
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 O14763
- Elsewhere: RCSB PDB 4OD2 · PDBe 4OD2 · UniProt O14763
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