Research workbench
11A1 antibody-peptide complex
Analyse 11A1 antibody-peptide complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7BXV
- Type
- protein
- Length
- 439 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab of the 11A1 antibody L chain; Fab of the 11A1 antibody H chain; Tyr-glu-val-his-his
- Pockets
- 5 · best druggability 0.54
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Fab of the 11A1 antibody L chain | protein | 217 | 6% helix, 52% strand | — |
| H | Fab of the 11A1 antibody H chain | protein | 217 | 11% helix, 52% strand | — |
| A | Tyr-glu-val-his-his | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
- EDO · 1,2-ethanediol · additive · 5 copies · chains L, H, A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 64 | 0.54 | 0.88 | 20 | empty |
| 2 | 263 | 0.51 | 0.75 | 41 | empty |
| 3 | 180 | 0.46 | 0.75 | 30 | empty |
| 4 | 103 | 0.39 | 0.75 | 27 | EDO |
| 5 | 88 | 0.32 | 0.74 | 21 | empty |
Interfaces
3 interfaces between chains.
- L–H · 1768 Ų buried · 15 hydrogen bonds · protein-protein
- H–A · 333 Ų buried · 8 hydrogen bonds · protein-protein
- L–A · 237 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 7BXV · 11A1 antibody-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 7BXV · PDBe 7BXV
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