Research workbench
Crystal Structure of Quaternary-Specific RSV-Neutralizing Human Antibody AM14
Analyse Crystal Structure of Quaternary-Specific RSV-Neutralizing Human Antibody AM14 in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4ZYK
- Type
- protein
- Length
- 858 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2
- Source
- Homo sapiens
- Molecule
- AM14 Fab heavy chain; AM14 light chain
- Ligands
- SO4
- Pockets
- 8 · best druggability 0.66
Structure
x-ray diffraction · resolution 2 · 4 distinct chains · 7% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | AM14 Fab heavy chain | protein | 214 | 8% helix, 52% strand | — |
| L | AM14 light chain | protein | 213 | 5% helix, 51% strand | — |
| A | AM14 Fab heavy chain | protein | 217 | 7% helix, 53% strand | — |
| B | AM14 light chain | protein | 214 | 6% helix, 50% strand | — |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 2 copies · chains H, L, B
- EDO · 1,2-ethanediol · additive · 5 copies · chains H, L, A, B
- ACT · Acetate ion · additive · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
8 pockets found on a 1 Å grid, 4 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 426 | 0.66 | 0.79 | 54 | empty |
| 2 | 504 | 0.64 | 0.77 | 41 | SO4 |
| 3 | 195 | 0.57 | 0.80 | 33 | empty |
| 4 | 64 | 0.54 | 0.88 | 22 | EDO |
| 5 | 161 | 0.44 | 0.75 | 21 | empty |
Interfaces
3 interfaces between chains.
- H–L · 1778 Ų buried · 14 hydrogen bonds · protein-protein
- A–B · 1775 Ų buried · 13 hydrogen bonds · protein-protein
- L–B · 902 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide (disulfide).
Compared structures
- 4ZYK · Crystal structure of quaternary-specific rsv-neutralizing human antibody AM14 · 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 4ZYK · PDBe 4ZYK
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