Research workbench
Binding of chloromethyl ketone substrate analogues to crystalline papain
Analyse Binding of chloromethyl ketone substrate analogues to crystalline papain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 6PAD
- Type
- protein
- Length
- 212 residues
- Chains
- 1
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain
- EC
- 3.4.22.2
- UniProt
- P00784
- Ligands
- 0PC
- Pockets
- 1 · best druggability 0.28
Structure
x-ray diffraction · 1 distinct chain · 25% helix, 18% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain (EC 3.4.22.2) | protein | 212 | 25% helix, 18% strand | P00784 |
Ligands and binding sites
- 0PC · Nalpha-[(benzyloxy)carbonyl]-N-[(1S)-3-chloro-1-methyl-2-oxopropyl]-L-phenylalaninamide · ligand · chains A
Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.
Pockets
1 pocket found on a 1 Å grid, 0 with a druggability of 0.5 or more.
| Volume (ų) | Druggability | Buriedness | Lining residues | Inside | |
|---|---|---|---|---|---|
| 1 | 61 | 0.28 | 0.73 | 22 | 0PC |
Modifications
Observed in the structure: 3 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 6PAD · PDBe 6PAD · UniProt P00784
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