MolNFT v1 · #104356 · protein
Neutrophil serine protease 4 (PRSS57) with val-leu-lys- chloromethylketone (vlk-cmk)
4Q80 · Serine protease 57: “Neutrophil serine protease 4 (PRSS57) with val-leu-lys- chloromethylketone (vlk-cmk)”. X-ray diffraction, 2 ligands (2YS, NAG), 3 pockets (best druggability 0.71). MolNFT v1 #104356 on GenesisL1: 3D structure…
- PDB
- 4Q80
- Type
- protein
- Length
- 466 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Serine protease 57
- EC
- 3.4.21.-
- UniProt
- Q6UWY2
- Ligands
- 2YS, NAG
- Pockets
- 3 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Serine protease 57 (EC 3.4.21.-) | protein | 233 | 12% helix, 35% strand | Q6UWY2 |
Ligands and binding sites
- 2YS · D-valyl-N-[(2S,3S)-7-amino-1-chloro-2-hydroxyheptan-3-yl]-L-leucinamide · ligand · 2 copies · chains A, B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 7 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 804 | 0.71 | 0.77 | 75 | 2YS |
| 2 | 71 | 0.37 | 0.77 | 15 | empty |
| 3 | 55 | 0.32 | 0.77 | 18 | empty |
Interfaces
1 interface between chains.
- A–B · 665 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 4 covalent, 4 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- 4Q80 · Neutrophil serine protease 4 (PRSS57) with val-leu-lys-chloromethylketone (VLK-cmk) · the same entry in another collection · chain A against A, TM-score 1.00
- Q6UWY2 · AlphaFold monomer V2.0 prediction for serine protease 57 (Q6UWY2) · a predicted model of the same protein · 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 Q6UWY2
- Elsewhere: RCSB PDB 4Q80 · PDBe 4Q80 · UniProt Q6UWY2
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