Research workbench
The structure of the anti-C-myc antibody 9E10 Fab fragment
Analyse The structure of the anti-C-myc antibody 9E10 Fab fragment in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2ORB
- Type
- protein
- Length
- 843 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Monoclonal anti-C-myc antibody 9E10
- Ligands
- SO4
- Pockets
- 7 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 5% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Monoclonal anti-C-myc antibody 9E10 | protein | 212 | 5% helix, 52% strand | — |
| H | Monoclonal anti-C-myc antibody 9E10 | protein | 212 | 6% helix, 52% strand | — |
| M | Monoclonal anti-C-myc antibody 9E10 | protein | 210 | 5% helix, 52% strand | — |
| I | Monoclonal anti-C-myc antibody 9E10 | protein | 209 | 6% helix, 51% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
7 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 556 | 0.63 | 0.75 | 54 | empty |
| 2 | 514 | 0.61 | 0.75 | 53 | empty |
| 3 | 329 | 0.57 | 0.76 | 43 | empty |
| 4 | 121 | 0.41 | 0.76 | 24 | empty |
| 5 | 111 | 0.39 | 0.75 | 28 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1867 Ų buried · 11 hydrogen bonds · protein-protein
- M–I · 1694 Ų buried · 9 hydrogen bonds · protein-protein
- H–I · 232 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 2ORB · The structure of the anti-c-myc antibody 9E10 Fab fragment · 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 2ORB · PDBe 2ORB
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