7FQK

Crystal Structure of human Legumain in complex with (2S)-N-[(3S)-5-amino-1-(1,3-oxazol-2-yl)-5-oxopent-1-yn-3-yl]-1-[1-[4-(trifluoromethoxy)phenyl]cyclopropanecarbonyl]pyrrolidine-2-carboxamide

• PDB DOI: https://doi.org/10.2210/pdb7FQK/pdb
• Deposition Group: G_1002245 ExploreG_1002245

• Classification: HYDROLASE/INHIBITOR
• Organism(s): Homo sapiens
• Expression System: Drosophila
• Mutation(s): No 


• Deposited: 2022-10-05 Released: 2023-10-11 
• Deposition Author(s): Ehler, A., Benz, J., Bartels, B., Rudolph, M.G.
• Funding Organization(s): F. Hoffmann-La Roche

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.233 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 

Literature

Crystal Structure of a human Legumain complex

Bartels, B., Kuhn, B., Benz, J., Rudolph, M.G.

To be published.

Biological Assembly 1  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 1 assigned by authors.

Biological Assembly Evidence: gel filtration

Biological Assembly 2  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 2 assigned by authors.

Biological Assembly 3  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 3 assigned by authors.

Biological Assembly 4  

Global Symmetry: Asymmetric - C1 
Global Stoichiometry: Monomer - A1 

Biological assembly 4 assigned by authors.

Macromolecule Content

• Total Structure Weight: 207.2 kDa 
• Atom Count: 9,215 
• Modelled Residue Count: 1,048 
• Deposited Residue Count: 1,776 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Legumain	A, B, C, D	444	Homo sapiens	Mutation(s): 0  Gene Names: LGMN, PRSC1 EC: 3.4.22.34
UniProt & NIH Common Fund Data Resources
Find proteins for Q99538 (Homo sapiens) Explore Q99538  Go to UniProtKB:  Q99538
PHAROS:  Q99538 GTEx:  ENSG00000100600
Glycosylation
Glycosylation Sites: 1		Go to GlyGen: Q99538-1

Oligosaccharides

Help

Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	3D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	E	2		N-Glycosylation
Glycosylation Resources
GlyTouCan:  G42666HT GlyCosmos:  G42666HT GlyGen:  G42666HT

Small Molecules

Ligands 4 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WS9 (Subject of Investigation/LOI)	G [auth A], J [auth B], M [auth C], P [auth D]	N-[(1E,3R)-5-amino-1-(1,3-oxazol-2-yl)-5-oxopent-1-en-3-yl]-1-{1-[4-(trifluoromethoxy)phenyl]cyclopropane-1-carbonyl}-L-prolinamide C24 H25 F3 N4 O5 NPUBRLWTCZFTGN-UHFFFAOYSA-N
NAG	H [auth A], K [auth B], Q [auth D]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
MES	L [auth B], N [auth D]	2-(N-MORPHOLINO)-ETHANESULFONIC ACID C6 H13 N O4 S SXGZJKUKBWWHRA-UHFFFAOYSA-N
EDO	F [auth A], I [auth B], O [auth D]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

Modified Residues  1 Unique
ID	Chains	Type	Formula	2D Diagram	Parent
SNN	A, B, C, D	L-PEPTIDE LINKING	C4 H6 N2 O2		ASN

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 1.97 Å
• R-Value Free: 0.233 
• R-Value Work: 0.194 
• R-Value Observed: 0.196 
• Space Group: P 4₃ 2₁ 2

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 102.489	α = 90
b = 102.489	β = 90
c = 330.991	γ = 90

Software Package:

Software Name	Purpose
XSCALE	data scaling
REFMAC	refinement
PDB_EXTRACT	data extraction
XDS	data reduction
XSCALE	data scaling
PHASER	phasing

Structure Validation

Entry History & Funding Information

Deposition Data

• Released Date: 2023-10-11 
Deposition Author(s): Ehler, A., Benz, J., Bartels, B., Rudolph, M.G.

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Funding Organization	Location	Grant Number
F. Hoffmann-La Roche	Switzerland	--

Revision History  

• Version 1.0: 2023-10-11
  Type: Initial release
  
• Version 2.0: 2023-11-15
  Changes: Advisory, Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-10-09
  Changes: Structure summary