Research workbench
Crystal structure of a papain-like cysteine protease ervatamin-a complexed with irreversible inhibitor E-64
Analyse Crystal structure of a papain-like cysteine protease ervatamin-a complexed with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3BCN
- Type
- protein
- Length
- 418 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Ervatamin-a
- EC
- 3.4.22.-
- UniProt
- A5YVK8
- Ligands
- E64
- Pockets
- 3 · best druggability 0.51
Structure
x-ray diffraction · 1 distinct chain · 19% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, B | Ervatamin-a (EC 3.4.22.-) | protein | 209 | 19% helix, 18% strand | A5YVK8 |
Ligands and binding sites
- E64 · N-[N-[1-hydroxycarboxyethyl-carbonyl]leucylamino-butyl]-guanidine · ligand · 2 copies · chains A, B
- BME · Beta-mercaptoethanol · additive · chains A
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 | 197 | 0.51 | 0.77 | 35 | E64 |
| 2 | 123 | 0.40 | 0.75 | 33 | empty |
| 3 | 66 | 0.39 | 0.80 | 14 | empty |
Interfaces
1 interface between chains.
- A–B · 639 Ų buried · 6 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 3 covalent (disulfide, covalent ligand, additive adduct).
Compared structures
- 3BCN · Crystal structure of a papain-like cysteine protease Ervatamin-A complexed with… · 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 A5YVK8
- Elsewhere: RCSB PDB 3BCN · PDBe 3BCN · UniProt A5YVK8
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