MolNFT v1 · #152372 · protein
Structure of bispecific Fc
6IFJ · Immunoglobulin gamma-1 heavy chain: “Structure of bispecific Fc”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 3 pockets (best druggability 0.33). MolNFT v1 #152372 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6IFJ
- Type
- protein
- Length
- 445 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Immunoglobulin gamma-1 heavy chain; 13-mer peptide
- UniProt
- P0DOX5
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 3 · best druggability 0.33
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 48% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Immunoglobulin gamma-1 heavy chain | protein | 209 | 11% helix, 48% strand | P0DOX5 |
| B | Immunoglobulin gamma-1 heavy chain | protein | 210 | 10% helix, 47% strand | P0DOX5 |
| C, D | 13-mer peptide | protein | 13 | 0% helix, 69% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 6 copies · chains A, B
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains A, B
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · 2 copies · chains A, B
- GOL · Glycerol · additive · 5 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 82 | 0.33 | 0.75 | 17 | empty |
| 2 | 65 | 0.31 | 0.76 | 19 | empty |
| 3 | 68 | 0.29 | 0.73 | 20 | empty |
Interfaces
3 interfaces between chains.
- A–B · 1101 Ų buried · 7 hydrogen bonds · protein-protein
- A–C · 646 Ų buried · 10 hydrogen bonds · protein-protein
- B–D · 638 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6IFJ · Structure of bispecific Fc · 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 6IFJ · PDBe 6IFJ · UniProt P0DOX5
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