Research workbench
Crystal structure of 101F Fab bound to 17-mer peptide epitope
Analyse Crystal structure of 101F Fab bound to 17-mer peptide epitope in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3O45
- Type
- protein
- Length
- 897 residues
- Chains
- 6
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mouse monoclonal antibody 101F 101F Fab light chain; Mouse monoclonal antibody 101F 101F…
- UniProt
- P03420
- Ligands
- SO4, NH2
- Pockets
- 8 · best druggability 0.65
Structure
x-ray diffraction · 5 distinct chains · 6% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| L | Mouse monoclonal antibody 101F 101F Fab light chain | protein | 218 | 7% helix, 54% strand | — |
| H, A | Mouse monoclonal antibody 101F 101F Fab heavy chain | protein | 220 | 7% helix, 51% strand | — |
| B | Mouse monoclonal antibody 101F 101F Fab light chain | protein | 217 | 5% helix, 54% strand | — |
| P | Fusion glycoprotein F1 | protein | 12 | 0% helix, 17% strand | P03420 |
| C | Fusion glycoprotein F1 | protein | 10 | 0% helix, 10% strand | P03420 |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 626 | 0.65 | 0.75 | 58 | empty |
| 2 | 627 | 0.64 | 0.75 | 60 | empty |
| 3 | 350 | 0.64 | 0.79 | 46 | SO4 |
| 4 | 323 | 0.57 | 0.76 | 39 | empty |
| 5 | 209 | 0.53 | 0.77 | 29 | empty |
Interfaces
9 interfaces between chains.
- L–H · 1962 Ų buried · 13 hydrogen bonds · protein-protein
- A–B · 1939 Ų buried · 16 hydrogen bonds · protein-protein
- H–A · 630 Ų buried · 7 hydrogen bonds · protein-protein
- H–P · 473 Ų buried · 6 hydrogen bonds · protein-protein
- A–C · 472 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 3O45 · Crystal Structure of 101F Fab Bound to 17-mer Peptide Epitope · 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
- Every structure of UniProt P03420
- Elsewhere: RCSB PDB 3O45 · PDBe 3O45 · UniProt P03420
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