MolNFT v1 · #154410 · protein
The complex structure of human IgG Fc and its binding repebody
6KA7: “The complex structure of human IgG Fc and its binding repebody”. X-ray diffraction, 4 ligands (NAG, MAN, BMA), 11 pockets (best druggability 0.63). MolNFT v1 #154410 on GenesisL1: 3D structure, binding sites and pockets in GL1X.
- PDB
- 6KA7
- Type
- protein
- Length
- 860 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Repebody; Immunoglobulin gamma-1 heavy chain
- UniProt
- P0DOX5
- Ligands
- NAG, MAN, BMA, FUC
- Pockets
- 11 · best druggability 0.63
Structure
x-ray diffraction · 4 distinct chains · 11% helix, 29% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Repebody | protein | 246 | 16% helix, 13% strand | — |
| B | Repebody | protein | 208 | 7% helix, 15% strand | — |
| C | Immunoglobulin gamma-1 heavy chain | protein | 198 | 11% helix, 45% strand | P0DOX5 |
| D | Immunoglobulin gamma-1 heavy chain | protein | 208 | 12% helix, 47% strand | P0DOX5 |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains C, D
- MAN · alpha-D-mannopyranose · sugar · 4 copies · chains C, D
- BMA · beta-D-mannopyranose · sugar · 2 copies · chains C, D
- FUC · alpha-L-fucopyranose · sugar · 2 copies
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 5 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 101 | 0.63 | 0.89 | 28 | empty |
| 2 | 246 | 0.58 | 0.79 | 26 | empty |
| 3 | 261 | 0.57 | 0.78 | 31 | empty |
| 4 | 122 | 0.57 | 0.84 | 28 | empty |
| 5 | 107 | 0.52 | 0.81 | 22 | empty |
Interfaces
3 interfaces between chains.
- C–D · 1119 Ų buried · 7 hydrogen bonds · protein-protein
- B–D · 914 Ų buried · 14 hydrogen bonds · protein-protein
- A–C · 896 Ų buried · 11 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 5 disulfide, 2 glycan (disulfide, N-glycosylation).
Compared structures
- 6KA7 · The complex structure of Human IgG Fc and its binding Repebody · 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 6KA7 · PDBe 6KA7 · UniProt P0DOX5
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