Research workbench
Crystal structure of the artificial protein affinger P17 (AF.P17) complexed with Fc fragment of human IgG
Analyse Crystal structure of the artificial protein affinger P17 (AF.P17) complexed… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- 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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