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Crystal structure of matriptase in complex with inhibitor
Analyse Crystal structure of matriptase in complex with inhibitor in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 4R0I
- Type
- protein
- Length
- 245 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Suppressor of tumorigenicity 14 protein; Serine protease, matriptase, membrane-type…
- EC
- 3.4.21.109
- UniProt
- Q9Y5Y6
- Ligands
- 3KM
- Pockets
- 1 · best druggability 0.40
Structure
x-ray diffraction · 2 distinct chains · 10% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Suppressor of tumorigenicity 14 protein (EC 3.4.21.109) | protein | 241 | 10% helix, 35% strand | Q9Y5Y6 |
| B | Serine protease, matriptase, membrane-type serine protease 1, mt-SP1 (EC 3.4.21.109) | protein | 4 | 0% helix, 0% strand | Q9Y5Y6 |
Ligands and binding sites
- 3KM · 3-({(2S)-3-[4-(2-aminoethyl)piperidin-1-yl]-2-[(naphthalen-2-ylsulfonyl)amino]-3-oxopropyl}oxy)benzenecarboximidamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 119 | 0.40 | 0.75 | 31 | 3KM |
Interfaces
1 interface between chains.
- A–B · 357 Ų buried · 5 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 4 disulfide (disulfide).
Compared structures
- 4R0I · CRYSTAL STRUCTURE of MATRIPTASE in COMPLEX WITH INHIBITOR · the same entry in another collection · chain A against A, TM-score 1.00
- Q9Y5Y6 · AlphaFold monomer V2.0 prediction for suppressor of tumorigenicity 14 protein (Q9Y5Y6) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 Q9Y5Y6
- Elsewhere: RCSB PDB 4R0I · PDBe 4R0I · UniProt Q9Y5Y6
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