Research workbench
Fc abvance: increasing our knowledge of antibody structural space to enable faster and better decision-making in antibody drug discovery.
Analyse Fc abvance: increasing our knowledge of antibody structural space to enable… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5WAV
- Type
- protein
- Length
- 414 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin gamma-1 heavy CHAIN,IMMUNOGLOBULIN gamma-1 heavy chain
- UniProt
- P0DOX5
- Ligands
- NAG, MAN, FUC
- Pockets
- 1 · best druggability 0.27
Structure
x-ray diffraction · 2 distinct chains · 12% helix, 47% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin gamma-1 heavy CHAIN,IMMUNOGLOBULIN gamma-1 heavy chain | protein | 207 | 12% helix, 48% strand | P0DOX5 |
| B | Immunoglobulin gamma-1 heavy CHAIN,IMMUNOGLOBULIN gamma-1 heavy chain | protein | 207 | 12% helix, 47% strand | P0DOX5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 6 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A
- GOL · Glycerol · additive · 3 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 51 | 0.27 | 0.75 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1141 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 5WAV · Fc AbVance: Increasing our knowledge of antibody structural space to enable faster and… · 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
- Every structure of UniProt P0DOX5
- Elsewhere: RCSB PDB 5WAV · PDBe 5WAV · UniProt P0DOX5
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