Research workbench
Crystal structure of Papain modify by achiral Ru(II)complex
Analyse Crystal structure of Papain modify by achiral Ru(II)complex in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6H8T
- Type
- protein
- Length
- 424 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v2 / PDB Bank
- Contract
- 0xd58B01f6C18086e5202cdC5D7Ad3E41790360102
- Owner
- 0xF4e1AA6f26B7DA48EeAD9B24a97927303eeA07b8
- Resolution
- 2.1
- Source
- Carica papaya
- Molecule
- Papain
- EC
- 3.4.22.2
- UniProt
- P00784
- Ligands
- YXZ, YXX, NA, CL, SO4
- Pockets
- 2 · best druggability 0.64
Structure
x-ray diffraction · resolution 2.1 · 1 distinct chain · 28% helix, 20% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A, J | Papain (EC 3.4.22.2) | protein | 212 | 28% helix, 20% strand | P00784 |
Ligands and binding sites
- YXZ · chloro[N,N-di(pyridin-2-yl-kappaN)pentane-1,5-diamine]ruthenium · ligand · chains A, J
- YXX · Chloro(1-{5-[di(pyridin-2-yl-kappan) amino]pentyl}pyrrolidine-2,5-dione)ruthenium · ligand · chains A, J
- NA · Sodium ion · metal · chains J
- CL · Chloride ion · ion · chains A
- SO4 · Sulfate ion · ion · chains A, J
- ACT · Acetate ion · additive · 9 copies · chains A, J
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
2 pockets found on a 1 Å grid, 2 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 252 | 0.64 | 0.82 | 45 | empty |
| 2 | 466 | 0.63 | 0.76 | 41 | ACT |
Interfaces
1 interface between chains.
- A–J · 652 Ų buried · 10 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 6 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
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 P00784
- Elsewhere: RCSB PDB 6H8T · PDBe 6H8T · UniProt P00784
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