7FQH

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

• PDB DOI: https://doi.org/10.2210/pdb7FQH/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., Hewings-David, S., Rudolph, M.G.
• Funding Organization(s): F. Hoffmann-La Roche

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Experimental Data Snapshot

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.272 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 

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.

Macromolecule Content

• Total Structure Weight: 154.48 kDa 
• Atom Count: 6,505 
• Modelled Residue Count: 782 
• Deposited Residue Count: 1,332 
• Unique protein chains: 1

Macromolecules

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Legumain	A, B, C [auth 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

Small Molecules

Ligands 3 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram
WR9 (Subject of Investigation/LOI)	D [auth A], G [auth B], J [auth D]	N-[(3S)-5-amino-5-oxopent-1-en-3-yl]-1-{1-[4-(cyclopropylmethoxy)phenyl]cyclopropane-1-carbonyl}-L-prolinamide C24 H31 N3 O4 SOCJRKDNYUYZLL-QUCCMNQESA-N
NAG	F [auth A], H [auth B]	2-acetamido-2-deoxy-beta-D-glucopyranose C8 H15 N O6 OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO	E [auth A], I [auth B]	1,2-ETHANEDIOL C2 H6 O2 LYCAIKOWRPUZTN-UHFFFAOYSA-N

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

Experimental Data & Validation

Experimental Data

• Method: X-RAY DIFFRACTION
• Resolution: 2.18 Å
• R-Value Free: 0.272 
• R-Value Work: 0.223 
• R-Value Observed: 0.226 
• Space Group: P 3 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 117.798	α = 90
b = 117.798	β = 90
c = 102.812	γ = 120

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., Hewings-David, S., 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: Atomic model, Data collection, Derived calculations
• Version 2.1: 2024-11-20
  Changes: Structure summary