Research workbench
Crystal structure of papain-E64-C complex. binding diversity of E64-C to papain S2 and S3 subsites
Analyse Crystal structure of papain-E64-C complex. binding diversity of E64-C to papain… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.
- PDB
- 1PPP
- 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
- E6C
- Pockets
- 1 · best druggability 0.30
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
- E6C · N-[1-hydroxycarboxyethyl-carbonyl]leucylamino-2-methyl-butane · ligand · chains A
- MOH · Methanol · additive · 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 | 53 | 0.30 | 0.76 | 16 | empty |
Modifications
Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).
Compared structures
- 1PPP · Crystal structure of papain-E64-C complex. binding diversity of E64-C to papain S2 and S3… · 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 A against A, TM-score 0.99
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 1PPP · PDBe 1PPP · UniProt P00784
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