Research workbench
Crystal structure of the zymogen matriptase catalytic domain
Analyse Crystal structure of the zymogen matriptase catalytic domain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5LYO
- Type
- protein
- Length
- 760 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Suppressor of tumorigenicity 14 protein
- EC
- 3.4.21.109
- UniProt
- Q9Y5Y6
- Ligands
- SO4
- Pockets
- 11 · best druggability 0.70
Structure
x-ray diffraction · 3 distinct chains · 10% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Suppressor of tumorigenicity 14 protein (EC 3.4.21.109) | protein | 253 | 10% helix, 33% strand | Q9Y5Y6 |
| B | Suppressor of tumorigenicity 14 protein (EC 3.4.21.109) | protein | 252 | 10% helix, 33% strand | Q9Y5Y6 |
| C | Suppressor of tumorigenicity 14 protein (EC 3.4.21.109) | protein | 255 | 10% helix, 32% strand | Q9Y5Y6 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 21 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
11 pockets found on a 1 Å grid, 3 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 786 | 0.70 | 0.76 | 72 | SO4 |
| 2 | 63 | 0.53 | 0.87 | 19 | empty |
| 3 | 161 | 0.51 | 0.79 | 22 | SO4 |
| 4 | 163 | 0.44 | 0.75 | 26 | SO4 |
| 5 | 111 | 0.42 | 0.77 | 22 | SO4 |
Interfaces
2 interfaces between chains.
- A–B · 426 Ų buried · 12 hydrogen bonds · protein-protein
- A–C · 300 Ų buried · 0 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 12 disulfide (disulfide).
Compared structures
- 5LYO · Crystal structure of the zymogen matriptase catalytic domain · 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 B against A, TM-score 0.93
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 5LYO · PDBe 5LYO · UniProt Q9Y5Y6
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