Research workbench
Structure of AMM01 Fab, an anti EBV GH/GL neutralizing antibody
Analyse Structure of AMM01 Fab, an anti EBV GH/GL neutralizing antibody in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6BLA
- Type
- protein
- Length
- 441 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- AMM01 Fab heavy chain; AMM01 Fab light chain
- Ligands
- CL
- Pockets
- 5 · best druggability 0.63
Structure
x-ray diffraction · 2 distinct chains · 9% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | AMM01 Fab heavy chain | protein | 226 | 9% helix, 49% strand | — |
| L | AMM01 Fab light chain | protein | 215 | 9% helix, 49% strand | — |
Ligands and binding sites
- CL · Chloride ion · ion · 6 copies · chains H, L
- EDO · 1,2-ethanediol · additive · 8 copies · chains H, L
- PEG · Di(hydroxyethyl)ether · additive · 4 copies · chains H, L
- GOL · Glycerol · additive · 2 copies · chains H, L
- TRS · 2-amino-2-hydroxymethyl-propane-1,3-diol · additive · chains H, L
- 2PE · Nonaethylene glycol · additive · 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 | 611 | 0.63 | 0.74 | 58 | TRS |
| 2 | 177 | 0.47 | 0.76 | 30 | PEG, EDO |
| 3 | 147 | 0.47 | 0.77 | 25 | empty |
| 4 | 53 | 0.37 | 0.80 | 18 | empty |
| 5 | 55 | 0.25 | 0.72 | 13 | CL |
Interfaces
1 interface between chains.
- H–L · 1903 Ų buried · 19 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 1 modified (disulfide, cyclization).
Compared structures
- 6BLA · Structure of AMM01 Fab, an anti EBV gH/gL neutralizing antibody · 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 6BLA · PDBe 6BLA
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