Research workbench
Structure of human fapalpha in complex with linagliptin
Analyse Structure of human fapalpha in complex with linagliptin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6Y0F
- Type
- protein
- Length
- 2,882 residues
- Chains
- 4
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prolyl endopeptidase fap
- EC
- 3.4.21.26, 3.4.14.5, 3.4.21.-
- UniProt
- Q12884
- Ligands
- 356, NAG, FUC, BMA
- Pockets
- 20 · best druggability 0.76
Structure
x-ray diffraction · 4 distinct chains · 18% helix, 36% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Prolyl endopeptidase fap (EC 3.4.21.26, 3.4.14.5, 3.4.21.-) | protein | 721 | 19% helix, 36% strand | Q12884 |
| B | Prolyl endopeptidase fap (EC 3.4.21.26, 3.4.14.5, 3.4.21.-) | protein | 719 | 19% helix, 36% strand | Q12884 |
| C | Prolyl endopeptidase fap (EC 3.4.21.26, 3.4.14.5, 3.4.21.-) | protein | 722 | 18% helix, 36% strand | Q12884 |
| D | Prolyl endopeptidase fap (EC 3.4.21.26, 3.4.14.5, 3.4.21.-) | protein | 720 | 18% helix, 36% strand | Q12884 |
Ligands and binding sites
- 356 · 8-[(3R)-3-Aminopiperidin-1-yl]-7-but-2-yn-1-yl-3-methyl-1-[(4-methylquinazolin-2-yl)methyl]-3,7-dihydro-1H-purine-2,6-d ione · ligand · 4 copies · chains A, B, C, D
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 21 copies · chains A, B, D, C
- FUC · alpha-L-fucopyranose · sugar · 3 copies · chains D
- BMA · beta-D-mannopyranose · sugar
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
20 pockets found on a 1 Å grid, 17 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 81 | 0.76 | 0.98 | 24 | empty |
| 2 | 77 | 0.75 | 0.98 | 22 | empty |
| 3 | 998 | 0.74 | 0.77 | 104 | 356 |
| 4 | 960 | 0.71 | 0.75 | 94 | empty |
| 5 | 949 | 0.71 | 0.75 | 85 | empty |
Interfaces
3 interfaces between chains.
- C–D · 2114 Ų buried · 26 hydrogen bonds · protein-protein
- A–B · 2113 Ų buried · 26 hydrogen bonds · protein-protein
- B–D · 152 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 15 glycan, 14 disulfide (N-glycosylation, disulfide).
Compared structures
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 Q12884
- Elsewhere: RCSB PDB 6Y0F · PDBe 6Y0F · UniProt Q12884
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