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Complex structure of tarocystatin and papain

Analyse Complex structure of tarocystatin and papain in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 3IMA
Type: protein
Length: 593 residues
Chains: 4
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Papain; Cysteine proteinase inhibitor
EC: 3.4.22.2
UniProt: P00784, Q8L5J8
Pockets: 2 · best druggability 0.35

Structure

x-ray diffraction · 3 distinct chains · 26% helix, 36% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, C	Papain (EC 3.4.22.2)	protein	212	27% helix, 22% strand	P00784
B	Cysteine proteinase inhibitor	protein	84	25% helix, 55% strand	Q8L5J8
D	Cysteine proteinase inhibitor	protein	85	24% helix, 55% strand	Q8L5J8

Ligands and binding sites

ACT · Acetate ion · additive · 3 copies · chains A, C

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

Pockets

2 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	77	0.35	0.76	17	empty
2	65	0.32	0.75	18	empty

Interfaces

3 interfaces between chains.

A–B · 913 Å² buried · 12 hydrogen bonds · protein-protein
C–D · 864 Å² buried · 13 hydrogen bonds · protein-protein
A–C · 50 Å² buried · 1 hydrogen bond · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 modified (disulfide, oxidation).

Compared structures

3IMA · Complex structure of tarocystatin and 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 1.00

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
Every structure of UniProt Q8L5J8
Elsewhere: RCSB PDB 3IMA · PDBe 3IMA · UniProt P00784 · UniProt Q8L5J8

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