Research workbench
Antibody 2G12 recognizes di-mannose equivalently in domain- and non- domain-exchanged forms, but only binds the HIV-1 glycan shield if domain-exchanged
Analyse Antibody 2G12 recognizes di-mannose equivalently in domain- and non… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3OAU
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Fab 2G12, heavy chain; Fab 2G12, light chain
- Ligands
- MAN, SO4
- Pockets
- 3 · best druggability 0.56
Structure
x-ray diffraction · 2 distinct chains · 7% helix, 51% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Fab 2G12, heavy chain | protein | 218 | 7% helix, 50% strand | — |
| L | Fab 2G12, light chain | protein | 212 | 6% helix, 52% strand | — |
Ligands and binding sites
- MAN · alpha-D-mannopyranose · sugar · 2 copies · chains H, L
- SO4 · Sulfate ion · ion · 2 copies · chains H
- GOL · Glycerol · additive · chains L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 365 | 0.56 | 0.75 | 47 | empty |
| 2 | 105 | 0.37 | 0.74 | 25 | empty |
| 3 | 111 | 0.36 | 0.74 | 22 | GOL |
Interfaces
1 interface between chains.
- H–L · 1957 Ų buried · 18 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 3OAU · Antibody 2G12 Recognizes Di-Mannose Equivalently in Domain- and Non-Domain-Exchanged… · 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 3OAU · PDBe 3OAU
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