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Crystal structure of the 13F6-1-2 Fab fragment bound to its ebola virus glycoprotein peptide epitope.
Analyse Crystal structure of the 13F6-1-2 Fab fragment bound to its ebola virus… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2QHR
- Type
- protein
- Length
- 451 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- 13F6-1-2 Fab fragment heavy chain; 13F6-1-2 Fab fragment V lambda X light chain; Envelope…
- UniProt
- P01844
- Pockets
- 5 · best druggability 0.56
Structure
x-ray diffraction · 3 distinct chains · 9% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | 13F6-1-2 Fab fragment heavy chain | protein | 222 | 10% helix, 50% strand | — |
| L | 13F6-1-2 Fab fragment V lambda X light chain | protein | 218 | 8% helix, 56% strand | P01844 |
| P | Envelope glycoprotein peptide | protein | 11 | 0% helix, 0% strand | — |
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 337 | 0.56 | 0.75 | 40 | empty |
| 2 | 97 | 0.42 | 0.78 | 18 | empty |
| 3 | 84 | 0.32 | 0.73 | 20 | empty |
| 4 | 52 | 0.28 | 0.75 | 13 | empty |
| 5 | 52 | 0.25 | 0.72 | 13 | empty |
Interfaces
3 interfaces between chains.
- H–L · 2127 Ų buried · 21 hydrogen bonds · protein-protein
- H–P · 639 Ų buried · 20 hydrogen bonds · protein-protein
- L–P · 325 Ų buried · 8 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 2QHR · Crystal structure of the 13F6-1-2 Fab fragment bound to its Ebola virus glycoprotein… · the same entry in another collection · chain H against H, TM-score 1.00
- P01844 · AlphaFold monomer V2.0 prediction for ig lambda-2 chain C region (P01844) · a predicted model of the same protein · chain L against A, TM-score 0.46
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 P01844
- Elsewhere: RCSB PDB 2QHR · PDBe 2QHR · UniProt P01844
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