MolNFT v1 · #140515 · protein
Crystal structure of the scfv antibody 4B08 with epitope peptide (mutation N3A)
5YD5 · Scfv 4B08: “Crystal structure of the scfv antibody 4B08 with epitope peptide (mutation N3A)”. X-ray diffraction, 1 ligand (SO4), 6 pockets (best druggability 0.66). MolNFT v1 #140515 on GenesisL1: 3D structure, binding sites and…
- PDB
- 5YD5
- Type
- protein
- Length
- 507 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scfv 4B08; Peptide epitope (mutation N3A)
- Ligands
- SO4
- Pockets
- 6 · best druggability 0.66
Structure
x-ray diffraction · 3 distinct chains · 4% helix, 46% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Scfv 4B08 | protein | 251 | 4% helix, 46% strand | — |
| B, D | Peptide epitope (mutation N3A) | protein | 8 | 0% helix, 0% strand | — |
| C | Scfv 4B08 | protein | 240 | 5% helix, 48% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 8 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
6 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 374 | 0.66 | 0.80 | 45 | SO4 |
| 2 | 69 | 0.32 | 0.75 | 17 | empty |
| 3 | 61 | 0.31 | 0.76 | 16 | empty |
| 4 | 81 | 0.31 | 0.73 | 19 | empty |
| 5 | 53 | 0.30 | 0.76 | 13 | empty |
Interfaces
4 interfaces between chains.
- A–C · 592 Ų buried · 10 hydrogen bonds · protein-protein
- A–B · 530 Ų buried · 10 hydrogen bonds · protein-protein
- C–D · 526 Ų buried · 9 hydrogen bonds · protein-protein
- B–C · 174 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5YD5 · Crystal structure of the scFv antibody 4B08 with epitope peptide (mutation N3A) · 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 5YD5 · PDBe 5YD5
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