Research workbench
The structure of the anti-C-myc antibody 9E10 Fab FRAGMENT/EPITOPE peptide complex reveals a novel binding mode dominated by the heavy chain hypervariable loops
Analyse The structure of the anti-C-myc antibody 9E10 Fab FRAGMENT/EPITOPE peptide… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2OR9
- Type
- protein
- Length
- 894 residues
- Chains
- 5
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal anti-C-myc antibody 9E10; Synthetic epitope peptide of 9E10
- Pockets
- 15 · best druggability 0.63
Structure
x-ray diffraction · 5 distinct chains · 5% helix, 53% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Monoclonal anti-C-myc antibody 9E10 | protein | 216 | 5% helix, 53% strand | — |
| H | Monoclonal anti-C-myc antibody 9E10 | protein | 221 | 5% helix, 54% strand | — |
| M | Monoclonal anti-C-myc antibody 9E10 | protein | 218 | 4% helix, 53% strand | — |
| I | Monoclonal anti-C-myc antibody 9E10 | protein | 228 | 7% helix, 52% strand | — |
| P | Synthetic epitope peptide of 9E10 | protein | 11 | 0% helix, 36% strand | — |
Pockets
15 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 565 | 0.63 | 0.75 | 49 | empty |
| 2 | 505 | 0.60 | 0.74 | 41 | empty |
| 3 | 131 | 0.46 | 0.77 | 27 | empty |
| 4 | 130 | 0.41 | 0.75 | 22 | empty |
| 5 | 72 | 0.38 | 0.78 | 20 | empty |
Interfaces
10 interfaces between chains.
- M–I · 2109 Ų buried · 19 hydrogen bonds · protein-protein
- L–H · 1950 Ų buried · 14 hydrogen bonds · protein-protein
- H–P · 748 Ų buried · 15 hydrogen bonds · protein-protein
- H–I · 405 Ų buried · 7 hydrogen bonds · protein-protein
- I–P · 178 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2OR9 · The structure of the anti-c-myc antibody 9E10 Fab fragment/epitope peptide complex… · the same entry in another collection · chain L against L, 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 2OR9 · PDBe 2OR9
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