MolNFT v1 · #18242 · protein
Crystal structure of papain-succinyl-gln-val-val-ala-ala-P- nitroanilide complex at 1.7 ångströms resolution: noncovalent binding mode of a common sequence of endogenous thiol protease inhibitors
1PIP: “Crystal structure of papain-succinyl-gln-val-val-ala-ala-P- nitroanilide complex at 1.7 ångströms resolution…”. X-ray diffraction, 1 ligand (NIT), 1 pocket (best druggability 0.45). MolNFT v1 #18242 on GenesisL1: 3D structure…
- PDB
- 1PIP
- Type
- protein
- Length
- 217 residues
- Chains
- 2
- Method
- x-ray diffraction
- Collection
- MolNFT v1 / PDB
- Contract
- 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
- Owner
- 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
- Molecule
- Papain; Succinyl-gln-val-val-ala-ala-P-nitroanilide
- EC
- 3.4.22.2
- UniProt
- P00784
- Ligands
- NIT
- Pockets
- 1 · best druggability 0.45
Structure
x-ray diffraction · 2 distinct chains · 24% helix, 19% strand (DSSP).
| Chain | Molecule | Type | Residues | Secondary structure | UniProt |
|---|---|---|---|---|---|
| A | Papain (EC 3.4.22.2) | protein | 212 | 25% helix, 19% strand | P00784 |
| B | Succinyl-gln-val-val-ala-ala-P-nitroanilide | protein | 5 | 0% helix, 0% strand | — |
Ligands and binding sites
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 | 81 | 0.45 | 0.81 | 20 | empty |
Interfaces
1 interface between chains.
- A–B · 247 Ų buried · 2 hydrogen bonds · protein-protein
Modifications
Observed in the structure: 3 disulfide, 2 covalent (disulfide, additive adduct, covalent ligand).
Compared structures
- 1PIP · Crystal structure of papain-succinyl-gln-val-val-ala-ala-P-nitroanilide complex at 1.7… · 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 1PIP · PDBe 1PIP · UniProt P00784
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