7FQI | pdb_00007fqi

Crystal Structure of human Legumain in complex with (2S)-N-[(1S)-3-amino-1-cyano-3-oxopropyl]-1-[1-[4-[(2,4-difluorophenyl)methoxy]phenyl]cyclopropanecarbonyl]pyrrolidine-2-carboxamide

PDB DOI: https://doi.org/10.2210/pdb7FQI/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

Experimental Data Snapshot

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free:
0.189 (Depositor), 0.197 (DCC)
R-Value Work:
0.167 (Depositor), 0.176 (DCC)
R-Value Observed:
0.168 (Depositor)

wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.1 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.

Macromolecule Content

Total Structure Weight: 155.71 kDa
Atom Count: 7,347
Modeled Residue Count: 790
Deposited Residue Count: 1,332
Unique protein chains: 1

Macromolecules

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(by identity cutoff) | 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Legumain	A, B, C	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
Entity Groups
Sequence Clusters	30% Identity50% Identity70% Identity90% Identity95% Identity100% Identity
UniProt Group	Q99538
Glycosylation
Glycosylation Sites: 1	Glycosylation Focus chain A Focus chain B Focus chain C	Go to GlyGen: Q99538-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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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	D, E, F	2		N-Glycosylation	Interactions Focus chain D Focus chain E Focus chain F Interactions & Density Focus chain D Focus chain E Focus chain F
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 2 Unique
ID	Chains	Name / Formula / InChI Key	2D Diagram	3D Interactions
WSN (Subject of Investigation/LOI) Query on WSN Download Ideal Coordinates CCD File SDF format, chain G [auth A] SDF format, chain K [auth B] SDF format, chain L [auth C] MOL2 format, chain G [auth A] MOL2 format, chain K [auth B] MOL2 format, chain L [auth C] mmCIF format, chain G [auth A] mmCIF format, chain K [auth B] mmCIF format, chain L [auth C]	G [auth A], K [auth B], L [auth C]	N-[(2R)-4-amino-1-imino-4-oxobutan-2-yl]-1-(1-{4-[(2,4-difluorophenyl)methoxy]phenyl}cyclopropane-1-carbonyl)-L-prolinamide C₂₆ H₂₈ F₂ N₄ O₄ UTRUAJSKSGNHPD-DIJIZMSBSA-N		Interactions Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth C] Interactions & Density Focus chain G [auth A] Focus chain K [auth B] Focus chain L [auth C]
EDO Query on EDO Download Ideal Coordinates CCD File SDF format, chain H [auth A] SDF format, chain I [auth A] SDF format, chain J [auth A] SDF format, chain M [auth C] SDF format, chain N [auth C] MOL2 format, chain H [auth A] MOL2 format, chain I [auth A] MOL2 format, chain J [auth A] MOL2 format, chain M [auth C] MOL2 format, chain N [auth C] mmCIF format, chain H [auth A] mmCIF format, chain I [auth A] mmCIF format, chain J [auth A] mmCIF format, chain M [auth C] mmCIF format, chain N [auth C]	H [auth A], I [auth A], J [auth A], M [auth C], N [auth C]	1,2-ETHANEDIOL C₂ H₆ O₂ LYCAIKOWRPUZTN-UHFFFAOYSA-N		Interactions Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth C] Focus chain N [auth C] Interactions & Density Focus chain H [auth A] Focus chain I [auth A] Focus chain J [auth A] Focus chain M [auth C] Focus chain N [auth C]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 1.45 Å
R-Value Free: 0.189 (Depositor), 0.197 (DCC)
R-Value Work: 0.167 (Depositor), 0.176 (DCC)
R-Value Observed: 0.168 (Depositor)

Space Group: C 1 2 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 229.51	α = 90
b = 67.093	β = 100.63
c = 79.12	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

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Ligand Structure Quality Assessment

Entry History & Funding Information

Deposition Data

Released Date: 2023-10-11

Deposition Author(s):

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

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
Version 2.1: 2024-12-25
Changes: Advisory, Derived calculations, Structure summary