MolNFT v1 · #140513 · protein
Crystal structure of the scfv antibody 4B08 with epitope peptide
5YD3 · Scfv 4B08: “Crystal structure of the scfv antibody 4B08 with epitope peptide”. X-ray diffraction, 1 ligand (SO4), 12 pockets (best druggability 0.77). MolNFT v1 #140513 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 5YD3
- Type
- protein
- Length
- 948 residues
- Chains
- 8
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Scfv 4B08; Epitope peptide
- Ligands
- SO4
- Pockets
- 12 · best druggability 0.77
Structure
x-ray diffraction · 7 distinct chains · 5% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Scfv 4B08 | protein | 231 | 5% helix, 50% strand | — |
| B, D | Epitope peptide | protein | 8 | 0% helix, 0% strand | — |
| C | Scfv 4B08 | protein | 229 | 4% helix, 50% strand | — |
| E | Scfv 4B08 | protein | 230 | 5% helix, 51% strand | — |
| F | Epitope peptide | protein | 9 | 0% helix, 0% strand | — |
| G | Scfv 4B08 | protein | 226 | 5% helix, 49% strand | — |
| H | Epitope peptide | protein | 7 | 0% helix, 0% strand | — |
Ligands and binding sites
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
12 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 1163 | 0.77 | 0.79 | 150 | SO4 |
| 2 | 369 | 0.61 | 0.77 | 51 | SO4 |
| 3 | 250 | 0.55 | 0.77 | 41 | empty |
| 4 | 195 | 0.49 | 0.76 | 26 | empty |
| 5 | 119 | 0.48 | 0.79 | 17 | empty |
Interfaces
9 interfaces between chains.
- A–G · 566 Ų buried · 6 hydrogen bonds · protein-protein
- A–B · 525 Ų buried · 12 hydrogen bonds · protein-protein
- C–D · 519 Ų buried · 10 hydrogen bonds · protein-protein
- E–F · 491 Ų buried · 13 hydrogen bonds · protein-protein
- C–G · 467 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 5YD3 · Crystal structure of the scFv antibody 4B08 with epitope peptide · 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 5YD3 · PDBe 5YD3
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