Research workbench
Crystal structure of the parasite protesase inhibitor chagasin in complex with papain
Analyse Crystal structure of the parasite protesase inhibitor chagasin in complex with… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 3E1Z
- Type
- protein
- Length
- 321 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Chagasin; Papain
- EC
- 3.4.22.2
- UniProt
- Q966X9, P00784
- Ligands
- ZN
- Pockets
- 4 · best druggability 0.46
Structure
x-ray diffraction · 2 distinct chains · 21% helix, 32% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Chagasin | protein | 109 | 6% helix, 52% strand | Q966X9 |
| B | Papain (EC 3.4.22.2) | protein | 212 | 28% helix, 22% strand | P00784 |
Ligands and binding sites
- ZN · Zinc ion · metal · chains A
- FMT · Formic acid · additive · 10 copies · chains A, B
- ACY · Acetic acid · additive · chains A, B
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
4 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 91 | 0.46 | 0.80 | 24 | empty |
| 2 | 94 | 0.39 | 0.76 | 20 | empty |
| 3 | 58 | 0.33 | 0.77 | 14 | FMT |
| 4 | 50 | 0.24 | 0.73 | 19 | empty |
Interfaces
1 interface between chains.
- A–B · 868 Ų buried · 13 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, additive adduct).
Compared structures
- 3E1Z · Crystal structure of the parasite protesase inhibitor chagasin in complex with papain · the same entry in another collection · chain A against A, TM-score 1.00
- P00784 · AlphaFold monomer V2.0 prediction for papain (P00784) · a predicted model of the same protein · chain B against A, TM-score 0.99
- Q966X9 · AlphaFold monomer V2.0 prediction for chagasin (Q966X9) · a predicted model of the same protein · chain A against A, TM-score 0.95
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 Q966X9
- Every structure of UniProt P00784
- Elsewhere: RCSB PDB 3E1Z · PDBe 3E1Z · UniProt Q966X9 · UniProt P00784
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