Research workbench
Crystal structure of the scfv antibody 4B08 with epitope peptide (mutation T6A)
Analyse Crystal structure of the scfv antibody 4B08 with epitope peptide (mutation T6A) in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5YD4
- Type
- protein
- Length
- 949 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scfv 4B08; Epitope peptide (mutation T6A)
- Ligands
- SO4
- Pockets
- 14 · best druggability 0.78
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Scfv 4B08 | protein | 232 | 5% helix, 50% strand | — |
| B, D | Epitope peptide (mutation T6A) | protein | 8 | 0% helix, 0% strand | — |
| C | Scfv 4B08 | protein | 229 | 5% helix, 50% strand | — |
| E | Scfv 4B08 | protein | 230 | 5% helix, 51% strand | — |
| F | Epitope peptide (mutation T6A) | protein | 9 | 0% helix, 0% strand | — |
| G | Scfv 4B08 | protein | 226 | 5% helix, 50% strand | — |
| H | Epitope peptide (mutation T6A) | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, C, G, E
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
14 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 737 | 0.78 | 0.83 | 101 | SO4 |
| 2 | 365 | 0.62 | 0.78 | 51 | SO4 |
| 3 | 266 | 0.56 | 0.77 | 42 | empty |
| 4 | 118 | 0.46 | 0.79 | 19 | empty |
| 5 | 187 | 0.45 | 0.74 | 26 | empty |
Interfaces
9 interfaces between chains.
- A–G · 627 Ų buried · 5 hydrogen bonds · protein-protein
- A–B · 529 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 516 Ų buried · 11 hydrogen bonds · protein-protein
- C–G · 499 Ų buried · 7 hydrogen bonds · protein-protein
- E–F · 489 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5YD4 · Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation T6A) · 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 5YD4 · PDBe 5YD4
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