Research workbench
Crystal structure of plant cysteine protease ervatamin-C complexed with irreversible inhibitor E-64 at 2.7 a resolution
Analyse Crystal structure of plant cysteine protease ervatamin-C complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 2PRE
- Type
- protein
- Length
- 416 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ervatamin-C
- EC
- 3.4.22.-
- UniProt
- A8DS38
- Ligands
- E64, SO4
- Pockets
- 2 · best druggability 0.71
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 22% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ervatamin-C (EC 3.4.22.-) | protein | 208 | 25% helix, 22% strand | A8DS38 |
Ligands and binding sites
- E64 · N-[N-[1-hydroxycarboxyethyl-carbonyl]leucylamino-butyl]-guanidine · ligand · 2 copies · chains A, B
- SO4 · Sulfate ion · ion · 6 copies · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 1 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 611 | 0.71 | 0.79 | 51 | empty |
| 2 | 121 | 0.46 | 0.78 | 24 | empty |
Interfaces
1 interface between chains.
- A–B · 614 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 8 disulfide, 2 covalent (disulfide, covalent ligand).
Compared structures
- 2PRE · Crystal structure of plant cysteine protease Ervatamin-C complexed with irreversible… · the same entry in another collection · 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 A8DS38
- Elsewhere: RCSB PDB 2PRE · PDBe 2PRE · UniProt A8DS38
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