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Structure of the precursor of a thermostable variant of papain at 2.6 angstroem resolution

Analyse Structure of the precursor of a thermostable variant of papain at 2.6 angstroem… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3TNX
Type: protein
Length: 620 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Papain
EC: 3.4.22.2
UniProt: P00784
Ligands: CL
Pockets: 3 · best druggability 0.41

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 17% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Papain (EC 3.4.22.2)	protein	310	33% helix, 17% strand	P00784

Ligands and binding sites

CL · Chloride ion · ion · chains A

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

Pockets

3 pockets found on a 1 Å grid, 0 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	89	0.41	0.78	18	empty
2	53	0.40	0.81	14	empty
3	52	0.30	0.76	16	empty

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

3TNX · Structure of the precursor of a thermostable variant of papain at 2.6 Angstroem resolution · 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 3TNX · PDBe 3TNX · UniProt P00784

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