Research workbench
Crystal structure of therapeutic mab AR20.5 in complex with MUC1 peptide
Analyse Crystal structure of therapeutic mab AR20.5 in complex with MUC1 peptide in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5T78
- Type
- protein
- Length
- 864 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab fragment AR20.5 - light chain; Fab fragment - AR20.5 - heavy chain; MUC1 glycopeptide
- Ligands
- NGA
- Pockets
- 9 · best druggability 0.78
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, C | Fab fragment AR20.5 - light chain | protein | 216 | 6% helix, 56% strand | — |
| B, D | Fab fragment - AR20.5 - heavy chain | protein | 209 | 6% helix, 52% strand | — |
| F, E | MUC1 glycopeptide | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- NGA · 2-acetamido-2-deoxy-beta-D-galactopyranose · sugar · 2 copies · chains A, B, F, C, D, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
9 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 935 | 0.78 | 0.81 | 89 | empty |
| 2 | 659 | 0.65 | 0.75 | 59 | empty |
| 3 | 175 | 0.57 | 0.81 | 35 | empty |
| 4 | 151 | 0.46 | 0.76 | 26 | empty |
| 5 | 67 | 0.44 | 0.82 | 21 | empty |
Interfaces
8 interfaces between chains.
- C–D · 1708 Ų buried · 12 hydrogen bonds · protein-protein
- A–B · 1692 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 437 Ų buried · 3 hydrogen bonds · protein-protein
- A–F · 391 Ų buried · 5 hydrogen bonds · protein-protein
- C–E · 387 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 glycan (disulfide, O-glycosylation).
Compared structures
- 5T78 · Crystal structure of therapeutic mAB AR20.5 in complex with MUC1 peptide · the same entry in another collection · chain C against C, 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 5T78 · PDBe 5T78
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