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Structure the bromelain protease from ananas comosus with a thiomethylated active cysteine

Analyse Structure the bromelain protease from ananas comosus with a thiomethylated… in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 6YCE
Type: protein
Length: 430 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Fbsb
UniProt: O23799
Ligands: NAG, BMA, XYS, FUC
Pockets: 2 · best druggability 0.78

Structure

x-ray diffraction · 1 distinct chain · 26% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Fbsb	protein	215	26% helix, 21% strand	O23799

Ligands and binding sites

NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 3 copies · chains A, B
BMA · beta-D-mannopyranose · sugar
XYS · alpha-D-xylopyranose · sugar
FUC · alpha-L-fucopyranose · sugar
IPA · Isopropyl alcohol · additive · chains B

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	808	0.78	0.82	84	empty
2	52	0.28	0.75	15	empty

Interfaces

1 interface between chains.

A–B · 590 Å² buried · 6 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 6 disulfide, 2 glycan, 2 modified (disulfide, N-glycosylation, methylation).

Compared structures

6YCE · Structure the bromelain protease from Ananas comosus with a thiomethylated active cysteine · the same entry in another collection · chain A against A, TM-score 1.00

Analyse

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Every structure of UniProt O23799
Elsewhere: RCSB PDB 6YCE · PDBe 6YCE · UniProt O23799

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