MolNFT v1 · #61957 · protein
X-ray structure of human prostasin in complex with benzoxazole warhead peptidomimic, lysine in P3
3E16: “X-ray structure of human prostasin in complex with benzoxazole warhead peptidomimic, lysine in P3”. X-ray diffraction, 1 ligand (B4C), 3 pockets (best druggability 0.47). MolNFT v1 #61957 on GenesisL1: 3D structure, binding sites…
- PDB
- 3E16
- Type
- protein
- Length
- 247 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Prostasin
- EC
- 3.4.21.-
- UniProt
- Q16651
- Ligands
- B4C
- Pockets
- 3 · best druggability 0.47
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 34% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| B | Prostasin (EC 3.4.21.-) | protein | 247 | 12% helix, 34% strand | Q16651 |
Ligands and binding sites
- B4C · benzyl [(1S)-5-amino-1-{[(1S)-1-({(1S)-5-amino-1-[(S)-1,3-benzoxazol-2-yl(hydroxy)methyl]pentyl}carbamoyl)-3-phenylpropyl]carbamoyl}pentyl]carbamate · ligand · chains B
- GOL · Glycerol · additive · chains B
- DMS · Dimethyl sulfoxide · additive · chains 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 | 120 | 0.47 | 0.79 | 35 | B4C |
| 2 | 96 | 0.35 | 0.74 | 17 | empty |
| 3 | 67 | 0.32 | 0.75 | 16 | empty |
Modifications
Observed in the structure: 4 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 3E16 · X-ray structure of human prostasin in complex with Benzoxazole warhead peptidomimic… · the same entry in another collection · chain B against B, TM-score 1.00
- Q16651 · AlphaFold monomer V2.0 prediction for prostasin (Q16651) · a predicted model of the same protein · chain B against A, TM-score 0.96
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 Q16651
- Elsewhere: RCSB PDB 3E16 · PDBe 3E16 · UniProt Q16651
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