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Crystal structure of a lona protease domain in complex with bortezomib

Analyse Crystal structure of a lona protease domain in complex with bortezomib in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 4YPM
Type: protein
Length: 290 residues
Chains: 1
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Lon protease
EC: 3.4.21.53
UniProt: A0A059VAZ3
Ligands: BO2, MG
Pockets: 1 · best druggability 0.45

Structure

x-ray diffraction · 1 distinct chain · 44% helix, 21% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A	Lon protease (EC 3.4.21.53)	protein	290	44% helix, 21% strand	A0A059VAZ3

Ligands and binding sites

BO2 · N-[(1R)-1-(dihydroxyboryl)-3-methylbutyl]-N-(pyrazin-2-ylcarbonyl)-L-phenylalaninamide · ligand · chains A
MG · Magnesium ion · metal · chains A
PEG · Di(hydroxyethyl)ether · additive · chains A
CIT · Citric acid · additive · chains A

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

Pockets

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

Pocket	Volume (Å³)	Druggability	Buriedness	Lining residues	Inside
1	83	0.45	0.81	26	BO2

Modifications

Observed in the structure: 1 covalent (covalent ligand).

Compared structures

4YPM · Crystal structure of a LonA protease domain in complex with bortezomib · the same entry in another collection · 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 A0A059VAZ3
Elsewhere: RCSB PDB 4YPM · PDBe 4YPM · UniProt A0A059VAZ3

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