MolNFT v1 · #103234 · protein

Binding of chloromethyl ketone substrate analogues to crystalline papain

4PAD: “Binding of chloromethyl ketone substrate analogues to crystalline papain”. X-ray diffraction, 1 ligand (TCK). MolNFT v1 #103234 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4PAD
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: TCK

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

TCK · N-[(1S)-5-amino-1-(chloroacetyl)pentyl]-4-methylbenzenesulfonamide · ligand · chains A

Binding sites are the residues within 4.5 Å of a ligand's heavy atoms.

Modifications

Observed in the structure: 3 disulfide, 1 covalent (disulfide, covalent ligand).

Compared structures

4PAD · Binding of chloromethyl ketone substrate analogues to crystalline 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 A against A, TM-score 0.98

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 4PAD · PDBe 4PAD · UniProt P00784

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