MolNFT v1 · #104995 · protein

Crystal structure of I86L mutant of papain

4QRG: “Crystal structure of I86L mutant of papain”. X-ray diffraction, 2 ligands (NA, CL), 2 pockets (best druggability 0.34). MolNFT v1 #104995 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 4QRG
Type: protein
Length: 602 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: NA, CL
Pockets: 2 · best druggability 0.34

Structure

x-ray diffraction · 2 distinct chains · 34% helix, 18% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Papain (EC 3.4.22.2)	protein	300	35% helix, 18% strand	P00784
B	Papain (EC 3.4.22.2)	protein	302	33% helix, 19% strand	P00784

Ligands and binding sites

NA · Sodium ion · metal · chains A
CL · Chloride ion · ion · 2 copies · chains A

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	56	0.34	0.78	16	empty
2	54	0.27	0.74	11	empty

Modifications

Observed in the structure: 6 disulfide (disulfide).

Compared structures

4QRG · Crystal structure of I86L mutant of 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 0.99

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 4QRG · PDBe 4QRG · UniProt P00784

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