MolNFT v1 · #140514 · protein
Crystal structure of the scfv antibody 4B08 with epitope peptide (mutation T6A)
5YD4 · Scfv 4B08: “Crystal structure of the scfv antibody 4B08 with epitope peptide (mutation T6A)”. X-ray diffraction, 1 ligand (SO4), 14 pockets (best druggability 0.78). MolNFT v1 #140514 on GenesisL1: 3D structure, binding sites and…
- 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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