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High resolution TMPRSS2 structure following acylation by nafamostat
Analyse High resolution TMPRSS2 structure following acylation by nafamostat in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 8V04
- Type
- protein
- Length
- 340 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.58
- Source
- Homo sapiens
- Molecule
- Transmembrane protease serine 2 non-catalytic chain; Transmembrane protease serine 2
- UniProt
- O15393
- Ligands
- GBS, NAG, FUC, CA, UNX
- Pockets
- 3 · best druggability 0.41
Structure
x-ray diffraction · resolution 1.58 · 2 distinct chains · 12% helix, 35% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Transmembrane protease serine 2 non-catalytic chain | protein | 102 | 14% helix, 31% strand | O15393 |
| B | Transmembrane protease serine 2 | protein | 238 | 12% helix, 36% strand | O15393 |
Ligands and binding sites
- GBS · 4-guanidinobenzoic acid · ligand · chains B
- NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A
- FUC · alpha-L-fucopyranose · sugar · chains A
- CA · Calcium ion · metal · chains B
- UNX · Unknown atom or ion · ion · chains A
- EDO · 1,2-ethanediol · additive · 9 copies · chains A, B
- CIT · Citric acid · additive · chains B
- PG4 · Tetraethylene glycol · 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 | 73 | 0.41 | 0.80 | 20 | UNX, EDO |
| 2 | 83 | 0.40 | 0.78 | 22 | GBS |
| 3 | 100 | 0.36 | 0.74 | 16 | empty |
Interfaces
1 interface between chains.
- A–B · 1094 Ų buried · 12 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 covalent, 1 glycan (disulfide, covalent ligand, N-glycosylation).
Compared structures
- O15393 · AlphaFold monomer V2.0 prediction for transmembrane protease serine 2 (O15393) · 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 O15393
- Elsewhere: RCSB PDB 8V04 · PDBe 8V04 · UniProt O15393
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