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Crystal structure of human legumain (aep) in complex with compound 11B

Analyse Crystal structure of human legumain (aep) in complex with compound 11B in the GL1X research workbench: secondary structure, accessibility, pockets, interfaces, conservation, variants, modifications, peptides, crosslinks and neighbours on the 3D structure.

PDB: 5LUA
Type: protein
Length: 522 residues
Chains: 2
Method: x-ray diffraction
Collection: MolNFT v1 / PDB
Contract: 0xDE3723766Bc32dcACD03C17BaA400A7B36837Eba
Owner: 0x3396CDB397284571d12822B4ae1189a8E22AAAAA
Molecule: Legumain
EC: 3.4.22.34
UniProt: Q99538
Ligands: SNN, 5KN, NAG
Pockets: 3 · best druggability 0.55

Structure

x-ray diffraction · 1 distinct chain · 33% helix, 20% strand (DSSP).

Chain	Molecule	Type	Residues	Secondary structure	UniProt
A, B	Legumain (EC 3.4.22.34)	protein	261	33% helix, 20% strand	Q99538

Ligands and binding sites

SNN · L-3-aminosuccinimide · ligand · 2 copies · chains A, B
5KN · 2,4-di(morpholin-4-yl)aniline · ligand · chains A, B
NAG · 2-acetamido-2-deoxy-beta-D-glucopyranose · sugar · 8 copies · chains A, B

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

Pockets

3 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	296	0.55	0.76	33	empty
2	157	0.43	0.74	20	empty
3	63	0.35	0.78	17	empty

Interfaces

1 interface between chains.

A–B · 593 Å² buried · 8 hydrogen bonds · protein-protein

Modifications

Observed in the structure: 5 glycan, 4 covalent (N-glycosylation, covalent ligand).

Compared structures

5LUA · Crystal structure of human legumain (AEP) in complex with compound 11b · the same entry in another collection · chain B against B, TM-score 1.00
Q99538 · AlphaFold monomer V2.0 prediction for legumain (Q99538) · 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 Q99538
Elsewhere: RCSB PDB 5LUA · PDBe 5LUA · UniProt Q99538

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