Research workbench
Three-dimensional structure of anti-ampicillin single chain fv fragment complexed with the hapten.
Analyse Three-dimensional structure of anti-ampicillin single chain fv fragment… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1H8S
- Type
- protein
- Length
- 436 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Mutant AL2 6E7P9G
- Ligands
- AIC, SO4
- Pockets
- 8 · best druggability 0.69
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Mutant AL2 6E7P9G | protein | 218 | 7% helix, 46% strand | — |
| B | Mutant AL2 6E7P9G | protein | 218 | 7% helix, 47% strand | — |
Ligands and binding sites
- AIC · (2S,5R,6R)-6-{[(2R)-2-amino-2-phenylethanoyl]amino}-3,3-dimethyl-7-oxo-4-thia-1-azabicyclo[3.2.0]heptane-2-carboxylic acid · ligand · chains A
- SO4 · Sulfate ion · ion · 2 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 691 | 0.69 | 0.77 | 57 | empty |
| 2 | 154 | 0.51 | 0.79 | 30 | empty |
| 3 | 98 | 0.50 | 0.81 | 17 | AIC |
| 4 | 95 | 0.43 | 0.78 | 19 | empty |
| 5 | 92 | 0.39 | 0.76 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 469 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 1H8S · Three-dimensional structure of anti-ampicillin single chain Fv fragment complexed with… · the same entry in another collection · chain A against A, 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 1H8S · PDBe 1H8S
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