Research workbench
Cocktail experiment a: fragments 63, 267, and 291 in complex with endothiapepsin
Analyse Cocktail experiment a: fragments 63, 267, and 291 in complex with endothiapepsin in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 5MB0
- Type
- protein
- Length
- 330 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Endothiapepsin
- EC
- 3.4.23.22
- UniProt
- P11838
- Ligands
- F91, 47V, F63
- Pockets
- 1 · best druggability 0.57
Structure
x-ray diffraction · 1 distinct chain · 12% helix, 45% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Endothiapepsin (EC 3.4.23.22) | protein | 330 | 12% helix, 45% strand | P11838 |
Ligands and binding sites
- F91 · N-(pyridin-4-ylmethyl)-2,3-dihydro-1,4-benzodioxin-6-amine · ligand · 2 copies · chains A
- 47V · 2,5-dimethyl-N-(pyridin-4-yl)furan-3-carboxamide · ligand · chains A
- F63 · N-methyl-1-[5-(pyridin-3-yloxy)furan-2-yl]methanamine · ligand · chains A
- DMS · Dimethyl sulfoxide · additive · 6 copies · chains A
- GOL · Glycerol · 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 | 311 | 0.57 | 0.76 | 38 | 47V, F91, F63 |
Modifications
Observed in the structure: 1 disulfide (disulfide).
Compared structures
- 5MB0 · Cocktail experiment A: fragments 63, 267, and 291 in complex with Endothiapepsin · 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 5MB0 · PDBe 5MB0 · UniProt P11838
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