MolNFT v1 · #128529 · protein

Streptomyces papain inhibitor (spi)

5NTB: “Streptomyces papain inhibitor (spi)”. X-ray diffraction, 1 ligand (SO4), 1 pocket (best druggability 0.60). MolNFT v1 #128529 on GenesisL1: 3D structure, binding sites and pockets in GL1X.

PDB: 5NTB
Type: protein
Length: 220 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Papain inhibitor
UniProt: P86242
Ligands: SO4
Pockets: 1 · best druggability 0.60

Structure

x-ray diffraction · 1 distinct chain · 15% helix, 45% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Papain inhibitor	protein	110	15% helix, 45% strand	P86242

Ligands and binding sites

SO4 · Sulfate ion · ion · 3 copies · chains A, B

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

Pockets

1 pocket found on a 1 Å grid, 1 with a druggability of 0.5 or more.

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	351	0.60	0.77	56	empty

Interfaces

1 interface between chains.

A–B · 397 Å² buried · 3 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 4 disulfide (disulfide).

Compared structures

5NTB · Streptomyces papain inhibitor (SPI) · the same entry in another collection · chain A against A, TM-score 1.00
P86242 · AlphaFold monomer V2.0 prediction for papain inhibitor (P86242) · 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 P86242
Elsewhere: RCSB PDB 5NTB · PDBe 5NTB · UniProt P86242

GL1X is a live explorer of the GenesisL1 blockchain. Turn on JavaScript for search, charts and interactive views.