MolNFT v1 · #117994 · protein
Structure of the murine antibody Fab 8E3 bound to the vaccinia virus A27 peptide 101-110
5EOR · Anti vaccinia virus A27 antibody 8E3 heavy chain: “Structure of the murine antibody Fab 8E3 bound to the vaccinia virus A27 peptide 101-110”. X-ray diffraction, 1 ligand (NA), 5 pockets (best druggability 0.57). MolNFT v1 #117994 on…
- PDB
- 5EOR
- Type
- protein
- Length
- 440 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Anti vaccinia virus A27 antibody 8E3 heavy chain; Anti vaccinia virus A27 antibody 8E3…
- Ligands
- NA
- Pockets
- 5 · best druggability 0.57
Structure
x-ray diffraction · 3 distinct chains · 6% helix, 54% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Anti vaccinia virus A27 antibody 8E3 heavy chain | protein | 214 | 4% helix, 54% strand | — |
| L | Anti vaccinia virus A27 antibody 8E3 light chain | protein | 217 | 7% helix, 56% strand | — |
| A | Protein A27 | protein | 9 | 0% helix, 11% strand | — |
Ligands and binding sites
- NA · Sodium ion · metal · chains H
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 451 | 0.57 | 0.73 | 54 | empty |
| 2 | 102 | 0.38 | 0.75 | 23 | empty |
| 3 | 68 | 0.33 | 0.76 | 16 | empty |
| 4 | 51 | 0.26 | 0.74 | 14 | empty |
| 5 | 50 | 0.25 | 0.73 | 14 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1832 Ų buried · 13 hydrogen bonds · protein-protein
- L–A · 478 Ų buried · 11 hydrogen bonds · protein-protein
- H–A · 353 Ų buried · 7 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 5EOR · Structure of the murine antibody Fab 8E3 bound to the vaccinia virus A27 peptide 101-110 · the same entry in another collection · chain H against H, 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 5EOR · PDBe 5EOR
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