MolNFT v1 · #83515 · protein
Crystal structure of the artificial protein affinger P17 (AF.P17) complexed with Fc fragment of human IgG
3WKN · Ig gamma-1 chain C region: “Crystal structure of the artificial protein affinger P17 (AF.P17) complexed with Fc fragment of human IgG”. X-ray diffraction, 5 ligands (NAG, MAN, BMA), 20 pockets (best druggability 0.72). MolNFT v1…
- PDB
- 3WKN
- Type
- protein
- Length
- 2,010 residues
- Chains
- 16
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ig gamma-1 chain C region; Affinger P17
- UniProt
- P01857
- Ligands
- NAG, MAN, BMA, GAL, FUC
- Pockets
- 20 · best druggability 0.72
Structure
x-ray diffraction · 7 distinct chains · 10% helix, 49% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| C, A, D, I, J, M | Ig gamma-1 chain C region | protein | 209 | 11% helix, 50% strand | P01857 |
| B, N | Ig gamma-1 chain C region | protein | 210 | 11% helix, 49% strand | P01857 |
| E | Affinger P17 | protein | 29 | 0% helix, 52% strand | — |
| F, K, O | Affinger P17 | protein | 46 | 9% helix, 48% strand | — |
| G, L | Affinger P17 | protein | 47 | 17% helix, 51% strand | — |
| H | Affinger P17 | protein | 32 | 13% helix, 50% strand | — |
| P | Affinger P17 | protein | 43 | 0% helix, 47% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 32 copies · chains C, B, A, D, I, J, M, N
- MAN · alpha-D-mannopyranose · sugar · 16 copies · chains C, B, A, I, D, J, M, N
- BMA · beta-D-mannopyranose · sugar · 8 copies · chains C, B, A, D, I, J, M, N
- GAL · beta-D-galactopyranose · sugar · 8 copies · chains C, B, A, D, I, J, M, N
- FUC · alpha-L-fucopyranose · sugar · 8 copies · chains C, J, A, I, P, N
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 7 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 259 | 0.72 | 0.87 | 43 | empty |
| 2 | 192 | 0.68 | 0.86 | 31 | empty |
| 3 | 469 | 0.64 | 0.78 | 39 | empty |
| 4 | 446 | 0.63 | 0.76 | 54 | empty |
| 5 | 207 | 0.55 | 0.79 | 30 | empty |
Interfaces
31 interfaces between chains.
- M–N · 1258 Ų buried · 7 hydrogen bonds · protein-protein
- A–D · 1216 Ų buried · 11 hydrogen bonds · protein-protein
- I–J · 1161 Ų buried · 6 hydrogen bonds · protein-protein
- C–B · 1131 Ų buried · 6 hydrogen bonds · protein-protein
- N–P · 796 Ų buried · 9 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 16 disulfide, 8 glycan (disulfide, N-glycosylation).
Compared structures
- 3WKN · Crystal structure of the artificial protein AFFinger p17 (AF.p17) complexed with Fc… · the same entry in another collection · chain C against C, 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 P01857
- Elsewhere: RCSB PDB 3WKN · PDBe 3WKN · UniProt P01857
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