MolNFT v1 · #170590 · protein
Structure the ananain protease from ananas comosus covalently bound to with the E64 inhibitor
6YCB: “Structure the ananain protease from ananas comosus covalently bound to with the E64 inhibitor”. X-ray diffraction, 1 ligand (SO4), 3 pockets (best druggability 0.53). MolNFT v1 #170590 on GenesisL1: 3D structure, binding sites and…
- PDB
- 6YCB
- Type
- protein
- Length
- 430 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ananain
- EC
- 3.4.22.31
- UniProt
- P80884
- Ligands
- SO4
- Pockets
- 3 · best druggability 0.53
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 21% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ananain (EC 3.4.22.31) | protein | 215 | 25% helix, 21% strand | P80884 |
Ligands and binding sites
- SO4 · Sulfate ion · ion · 3 copies · chains A, B
- GOL · Glycerol · additive · 3 copies · chains A, B
- TLA · L(+)-tartaric acid · additive · 3 copies · chains A, 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, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 207 | 0.53 | 0.78 | 31 | empty |
| 2 | 78 | 0.39 | 0.78 | 18 | empty |
| 3 | 51 | 0.37 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 427 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 2 modified (disulfide, oxidation).
Compared structures
- 6YCB · Structure the ananain protease from Ananas comosus covalently bound to with the E64… · the same entry in another collection · chain A against A, TM-score 1.00
- P80884 · AlphaFold monomer V2.0 prediction for ananain (P80884) · a predicted model of the same protein · chain A against A, TM-score 0.99
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 P80884
- Elsewhere: RCSB PDB 6YCB · PDBe 6YCB · UniProt P80884
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