7FQL | pdb_00007fql

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/pdb7FQL/pdb
Deposition Group: G_1002245 | Explore G_1002245

Classification: HYDROLASE
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: 2.53 Å
R-Value Free:
0.252 (Depositor), 0.262 (DCC)
R-Value Work:
0.192 (Depositor), 0.201 (DCC)
R-Value Observed:
0.195 (Depositor)

Starting Model: other
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wwPDB Validation 3D Report Full Report

Ligand Structure Quality Assessment

This is version 2.2 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: 414.84 kDa
Atom Count: 17,343
Modeled Residue Count: 2,090
Deposited Residue Count: 3,552
Unique protein chains: 1

Macromolecules

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| 3D Structure

Entity ID: 1
Molecule	Chains	Sequence Length	Organism	Details	Image
Legumain	A, B, C, D, E A, B, C, D, E, F, G, H	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% Identity 50% Identity 70% Identity 90% Identity 95% Identity 100% Identity
UniProt Group	Q99538
Glycosylation
Glycosylation Sites: 2	Glycosylation Focus chain A Focus chain B Focus chain C Focus chain D Focus chain E Focus chain F Focus chain G Focus chain H	Go to GlyGen: Q99538-1
Sequence Annotations Expand
Reference Sequence

Oligosaccharides

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Entity ID: 2
Molecule	Chains	Length	2D Diagram	Glycosylation	D Interactions
2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose	I, J	2		N-Glycosylation	Interactions Focus chain I Focus chain J Interactions & Density Focus chain I Focus chain J
Glycosylation Resources
GlyTouCan: G42666HT GlyCosmos: G42666HT GlyGen: G42666HT

Small Molecules

Ligands 3 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 X [auth F] SDF format, chain T [auth E] SDF format, chain R [auth D] SDF format, chain P [auth C] SDF format, chain M [auth B] SDF format, chain K [auth A] SDF format, chain GA [auth H] SDF format, chain CA [auth G] MOL2 format, chain X [auth F] MOL2 format, chain T [auth E] MOL2 format, chain R [auth D] MOL2 format, chain P [auth C] MOL2 format, chain M [auth B] MOL2 format, chain K [auth A] MOL2 format, chain GA [auth H] MOL2 format, chain CA [auth G] mmCIF format, chain X [auth F] mmCIF format, chain T [auth E] mmCIF format, chain R [auth D] mmCIF format, chain P [auth C] mmCIF format, chain M [auth B] mmCIF format, chain K [auth A] mmCIF format, chain GA [auth H] mmCIF format, chain CA [auth G]	CA [auth G] GA [auth H] K [auth A] M [auth B] P [auth C] CA [auth G], GA [auth H], K [auth A], M [auth B], P [auth C], R [auth D], T [auth E], X [auth F]	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 CA [auth G] Focus chain GA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain X [auth F] Interactions & Density Focus chain CA [auth G] Focus chain GA [auth H] Focus chain K [auth A] Focus chain M [auth B] Focus chain P [auth C] Focus chain R [auth D] Focus chain T [auth E] Focus chain X [auth F]
NAG Query on NAG Download:Ideal Coordinates CCD File SDF format, chain Y [auth F] SDF format, chain W [auth F] SDF format, chain U [auth E] SDF format, chain S [auth D] SDF format, chain O [auth C] SDF format, chain L [auth A] SDF format, chain IA [auth H] SDF format, chain HA [auth H] SDF format, chain DA [auth G] SDF format, chain BA [auth G] MOL2 format, chain Y [auth F] MOL2 format, chain W [auth F] MOL2 format, chain U [auth E] MOL2 format, chain S [auth D] MOL2 format, chain O [auth C] MOL2 format, chain L [auth A] MOL2 format, chain IA [auth H] MOL2 format, chain HA [auth H] MOL2 format, chain DA [auth G] MOL2 format, chain BA [auth G] mmCIF format, chain Y [auth F] mmCIF format, chain W [auth F] mmCIF format, chain U [auth E] mmCIF format, chain S [auth D] mmCIF format, chain O [auth C] mmCIF format, chain L [auth A] mmCIF format, chain IA [auth H] mmCIF format, chain HA [auth H] mmCIF format, chain DA [auth G] mmCIF format, chain BA [auth G]	BA [auth G] DA [auth G] HA [auth H] IA [auth H] L [auth A] BA [auth G], DA [auth G], HA [auth H], IA [auth H], L [auth A], O [auth C], S [auth D], U [auth E], W [auth F], Y [auth F]	2-acetamido-2-deoxy-beta-D-glucopyranose C₈ H₁₅ N O₆ OVRNDRQMDRJTHS-FMDGEEDCSA-N		Interactions Focus chain BA [auth G] Focus chain DA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain L [auth A] Focus chain O [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth F] Interactions & Density Focus chain BA [auth G] Focus chain DA [auth G] Focus chain HA [auth H] Focus chain IA [auth H] Focus chain L [auth A] Focus chain O [auth C] Focus chain S [auth D] Focus chain U [auth E] Focus chain W [auth F] Focus chain Y [auth F]
SO4 Query on SO4 Download:Ideal Coordinates CCD File SDF format, chain V [auth E] SDF format, chain Z [auth F] SDF format, chain Q [auth C] SDF format, chain N [auth B] SDF format, chain JA [auth H] SDF format, chain FA [auth G] SDF format, chain EA [auth G] SDF format, chain AA [auth F] MOL2 format, chain V [auth E] MOL2 format, chain Z [auth F] MOL2 format, chain Q [auth C] MOL2 format, chain N [auth B] MOL2 format, chain JA [auth H] MOL2 format, chain FA [auth G] MOL2 format, chain EA [auth G] MOL2 format, chain AA [auth F] mmCIF format, chain V [auth E] mmCIF format, chain Z [auth F] mmCIF format, chain Q [auth C] mmCIF format, chain N [auth B] mmCIF format, chain JA [auth H] mmCIF format, chain FA [auth G] mmCIF format, chain EA [auth G] mmCIF format, chain AA [auth F]	AA [auth F] EA [auth G] FA [auth G] JA [auth H] N [auth B] AA [auth F], EA [auth G], FA [auth G], JA [auth H], N [auth B], Q [auth C], V [auth E], Z [auth F]	SULFATE ION O₄ S QAOWNCQODCNURD-UHFFFAOYSA-L		Interactions Focus chain AA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain JA [auth H] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth E] Focus chain Z [auth F] Interactions & Density Focus chain AA [auth F] Focus chain EA [auth G] Focus chain FA [auth G] Focus chain JA [auth H] Focus chain N [auth B] Focus chain Q [auth C] Focus chain V [auth E] Focus chain Z [auth F]

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

Experimental Data & Validation

Experimental Data

Method: X-RAY DIFFRACTION
Resolution: 2.53 Å
R-Value Free: 0.252 (Depositor), 0.262 (DCC)
R-Value Work: 0.192 (Depositor), 0.201 (DCC)
R-Value Observed: 0.195 (Depositor)

Space Group: P 1 2₁ 1

Unit Cell:

Length ( Å )	Angle ( ˚ )
a = 89.301	α = 90
b = 131.935	β = 90.25
c = 117.677	γ = 90

Software Package:

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

Structure Validation

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Ligand Structure Quality Assessment

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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
Version 2.2: 2026-02-18
Changes: Refinement description