Research workbench
Crystal structure of the extracellular domain of MSPL/TMPRSS13 in complex with dec-RVKR-cmk inhibitor
Analyse Crystal structure of the extracellular domain of MSPL/TMPRSS13 in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6KD5
- Type
- protein
- Length
- 373 residues
- Chains
- 3
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.6
- Source
- Homo sapiens; SYNTHETIC CONSTRUCT
- Molecule
- Transmembrane protease serine 13; Decanoyl-arg-val-lys-arg-chloromethylketone inhibitor
- EC
- 3.4.21.-
- UniProt
- Q9BYE2
- Ligands
- NAG, FUC, CA, SO4
- Pockets
- 5 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.6 · 3 distinct chains · 9% helix, 33% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transmembrane protease serine 13 (EC 3.4.21.-) | protein | 131 | 9% helix, 29% strand | Q9BYE2 |
| B | Transmembrane protease serine 13 (EC 3.4.21.-) | protein | 238 | 9% helix, 36% strand | Q9BYE2 |
| C | Decanoyl-arg-val-lys-arg-chloromethylketone inhibitor | protein | 4 | 0% helix, 25% strand | — |
Ligands and binding sites
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
- FUC · alpha-L-fucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains A
- SO4 · Sulfate ion · ion · 7 copies · chains A, B, C
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
5 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 174 | 0.64 | 0.84 | 37 | empty |
| 2 | 200 | 0.46 | 0.74 | 31 | empty |
| 3 | 114 | 0.37 | 0.73 | 18 | SO4 |
| 4 | 75 | 0.35 | 0.76 | 16 | empty |
| 5 | 53 | 0.28 | 0.75 | 16 | empty |
Interfaces
2 interfaces between chains.
- A–B · 1861 Ų buried · 21 hydrogen bonds · protein-protein
- B–C · 445 Ų buried · 17 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 9 disulfide, 2 glycan, 1 modified (disulfide, N-glycosylation, nonstandard).
Compared structures
- 6KD5 · Crystal structure of the extracellular domain of MSPL/TMPRSS13 in complex with… · the same entry in another collection · chain A against A, TM-score 1.00
- Q9BYE2 · AlphaFold monomer V2.0 prediction for transmembrane protease serine 13 (Q9BYE2) · a predicted model of the same protein · chain B against A, TM-score 0.97
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 Q9BYE2
- Elsewhere: RCSB PDB 6KD5 · PDBe 6KD5 · UniProt Q9BYE2
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