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


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 

wwPDB Validation   3D Report Full Report


Ligand Structure Quality Assessment 


This is version 2.0 of the entry. See complete history


Literature

Crystal Structure of a human Legumain complex

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

To be published.

Macromolecules
Find similar proteins by:  (by identity cutoff)  |  3D Structure
Entity ID: 1
MoleculeChains Sequence LengthOrganismDetailsImage
LegumainA,
B,
C [auth D]
444Homo sapiensMutation(s): 0 
Gene Names: LGMNPRSC1
EC: 3.4.22.34
UniProt & NIH Common Fund Data Resources
Find proteins for Q99538 (Homo sapiens)
Go to UniProtKB:  Q99538
PHAROS:  Q99538
GTEx:  ENSG00000100600 
Glycosylation
Glycosylation Sites: 1Go to GlyGen: Q99538-1
Sequence Annotations
Expand
  • Reference Sequence
Small Molecules
Ligands 3 Unique
IDChains Name / Formula / InChI Key2D Diagram3D Interactions
WR9 (Subject of Investigation/LOI)
Query on WR9

Download Ideal Coordinates CCD File 
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
Query on NAG

Download Ideal Coordinates CCD File 
F [auth A],
H [auth B]
2-acetamido-2-deoxy-beta-D-glucopyranose
C8 H15 N O6
OVRNDRQMDRJTHS-FMDGEEDCSA-N
EDO
Query on EDO

Download Ideal Coordinates CCD File 
E [auth A],
I [auth B]
1,2-ETHANEDIOL
C2 H6 O2
LYCAIKOWRPUZTN-UHFFFAOYSA-N
Modified Residues  1 Unique
IDChains TypeFormula2D DiagramParent
SNN
Query on SNN
A,
B,
C [auth D]
L-PEPTIDE LINKINGC4 H6 N2 O2ASN
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 = 117.798α = 90
b = 117.798β = 90
c = 102.812γ = 120
Software Package:
Software NamePurpose
XSCALEdata scaling
REFMACrefinement
PDB_EXTRACTdata extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing

Structure Validation

View Full Validation Report



Ligand Structure Quality Assessment 


Entry History & Funding Information

Deposition Data


Funding OrganizationLocationGrant Number
F. Hoffmann-La RocheSwitzerland--

Revision History  (Full details and data files)

  • Version 1.0: 2023-10-11
    Type: Initial release
  • Version 2.0: 2023-11-15
    Changes: Atomic model, Data collection, Derived calculations