MolNFT v1 · #149954 · protein
High-resolution structure of a therapeutic full-length anti-npra antibody with exceptional conformational diversity
6GFE · Immunoglobulin gamma-4 heavy chain: “High-resolution structure of a therapeutic full-length anti-npra antibody with exceptional conformational…”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 17 pockets (best druggability 0.68).…
- PDB
- 6GFE
- Type
- protein
- Length
- 1,285 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin gamma-4 heavy chain; Immunoglobulin gamma-4 light chain
- Ligands
- NAG, MAN, BMA, FUC, CA
- Pockets
- 17 · best druggability 0.68
Structure
x-ray diffraction · 3 distinct chains · 8% helix, 52% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| H | Immunoglobulin gamma-4 heavy chain | protein | 429 | 9% helix, 51% strand | — |
| K | Immunoglobulin gamma-4 heavy chain | protein | 426 | 9% helix, 52% strand | — |
| L, M | Immunoglobulin gamma-4 light chain | protein | 215 | 7% helix, 53% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains H, K
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains H, K
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains H, K
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains H, L, K
- CA · Calcium ion · metal · 2 copies · chains H, K
- ACT · Acetate ion · additive · 3 copies · chains K, M, H, L
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
17 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 345 | 0.68 | 0.82 | 41 | empty |
| 2 | 486 | 0.64 | 0.76 | 48 | empty |
| 3 | 476 | 0.57 | 0.73 | 64 | empty |
| 4 | 72 | 0.54 | 0.87 | 21 | empty |
| 5 | 342 | 0.54 | 0.74 | 45 | empty |
Interfaces
4 interfaces between chains.
- H–L · 2180 Ų buried · 21 hydrogen bonds · protein-protein
- K–M · 1821 Ų buried · 16 hydrogen bonds · protein-protein
- H–K · 1186 Ų buried · 7 hydrogen bonds · protein-protein
- K–L · 517 Ų buried · 4 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 14 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6GFE · High-resolution Structure of a therapeutic full-length anti-NPRA Antibody with… · 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 6GFE · PDBe 6GFE
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