Research workbench
Endothiapepsin in complex with compound TL00150 at room-temperature (temperature ramping up structure 2)
Analyse Endothiapepsin in complex with compound TL00150 at room-temperature… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 7QMS
- Type
- protein
- Length
- 330 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 1.79
- Source
- Cryphonectria parasitica
- Molecule
- Endothiapepsin
- EC
- 3.4.23.22
- UniProt
- P11838
- Ligands
- U1H
- Pockets
- 1 · best druggability 0.59
Structure
x-ray diffraction · resolution 1.79 · 1 distinct chain · 11% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endothiapepsin (EC 3.4.23.22) | protein | 330 | 11% helix, 45% strand | P11838 |
Ligands and binding sites
- U1H · [4-(trifluoromethyl)phenyl]methanamine · ligand · 2 copies · chains A
- DMS · Dimethyl sulfoxide · additive · 4 copies · chains A
- PG5 · 1-methoxy-2-[2-(2-methoxy-ethoxy]-ethane · additive · 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 340 | 0.59 | 0.76 | 38 | U1H, PG5, DMS |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 7QMS · Endothiapepsin in complex with compound TL00150 at room-temperature (temperature ramping… · the same entry in another collection · chain A against A, TM-score 1.00
- P11838 · AlphaFold monomer V2.0 prediction for endothiapepsin (P11838) · 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 P11838
- Elsewhere: RCSB PDB 7QMS · PDBe 7QMS · UniProt P11838
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