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- PDB-7fqj: Crystal Structure of human Legumain in complex with (2S)-N-[(1S)-... -

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Entry
Database: PDB / ID: 7fqj
TitleCrystal 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
ComponentsLegumain
KeywordsHYDROLASE/INHIBITOR / CYSTEINE PROTEASE / ALLOSTERIC INHIBITOR / ASPARAGINYL ENDOPEPTIDASE / ALZHEIMER'S DISEASE / HYDROLASE / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / self proteolysis / endolysosome lumen / response to acidic pH ...negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / self proteolysis / endolysosome lumen / response to acidic pH / activation of cysteine-type endopeptidase activity / dendritic spine organization / positive regulation of monocyte chemotaxis / Trafficking and processing of endosomal TLR / positive regulation of endothelial cell chemotaxis / negative regulation of multicellular organism growth / cellular response to hepatocyte growth factor stimulus / associative learning / protein maturation / endopeptidase activator activity / cellular response to calcium ion / MHC class II antigen presentation / positive regulation of mitotic cell cycle / lysosomal lumen / proteolysis involved in protein catabolic process / positive regulation of long-term synaptic potentiation / tau protein binding / memory / cellular response to amyloid-beta / antigen processing and presentation of exogenous peptide antigen via MHC class II / late endosome / apical part of cell / peptidase activity / negative regulation of neuron apoptotic process / lysosome / cysteine-type endopeptidase activity / negative regulation of gene expression / positive regulation of cell population proliferation / perinuclear region of cytoplasm / proteolysis / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
: / Legumain, prodomain / Legumain prodomain superfamily / Asparaginyl endopeptidase / Peptidase C13, legumain / Peptidase C13 family
Similarity search - Domain/homology
CITRATE ANION / Chem-WSN / Legumain
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsEhler, A. / Benz, J. / Bartels, B. / Rudolph, M.G.
Funding support Switzerland, 1items
OrganizationGrant numberCountry
F. Hoffmann-La Roche Switzerland
CitationJournal: To be published
Title: Crystal Structure of a human Legumain complex
Authors: Bartels, B. / Kuhn, B. / Benz, J. / Rudolph, M.G.
History
DepositionOct 5, 2022Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 11, 2023Provider: repository / Type: Initial release
Revision 2.0Nov 15, 2023Group: Atomic model / Data collection / Derived calculations
Category: atom_site / chem_comp_atom ...atom_site / chem_comp_atom / chem_comp_bond / pdbx_validate_rmsd_angle / pdbx_validate_torsion / struct_conn
Item: _atom_site.auth_atom_id / _atom_site.label_atom_id ..._atom_site.auth_atom_id / _atom_site.label_atom_id / _chem_comp_atom.atom_id / _chem_comp_bond.atom_id_1 / _chem_comp_bond.atom_id_2 / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr2_label_atom_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Legumain
B: Legumain
C: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)155,98618
Polymers152,6333
Non-polymers3,35315
Water11,962664
1
A: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0926
Polymers50,8781
Non-polymers1,2145
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
B: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)52,0145
Polymers50,8781
Non-polymers1,1364
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
3
C: Legumain
hetero molecules


Theoretical massNumber of molelcules
Total (without water)51,8807
Polymers50,8781
Non-polymers1,0026
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)229.393, 66.570, 79.108
Angle α, β, γ (deg.)90.00, 100.93, 90.00
Int Tables number5
Space group name H-MC121
Components on special symmetry positions
IDModelComponents
11A-504-

PG4

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Components

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Protein , 1 types, 3 molecules ABC

#1: Protein Legumain / Asparaginyl endopeptidase / Protease / cysteine 1


Mass: 50877.672 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: LGMN, PRSC1 / Plasmid: pExpreS2.1_hLGMN(18-433)_C-VD-8xHis / Production host: Drosophila melanogaster (fruit fly) / Strain (production host): ExpreS2 / References: UniProt: Q99538, legumain

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Sugars , 2 types, 3 molecules

#2: Polysaccharide 2-acetamido-2-deoxy-beta-D-glucopyranose-(1-4)-2-acetamido-2-deoxy-beta-D-glucopyranose


Type: oligosaccharide / Mass: 424.401 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
DescriptorTypeProgram
DGlcpNAcb1-4DGlcpNAcb1-Glycam Condensed SequenceGMML 1.0
WURCS=2.0/1,2,1/[a2122h-1b_1-5_2*NCC/3=O]/1-1/a4-b1WURCSPDB2Glycan 1.1.0
[]{[(4+1)][b-D-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}}LINUCSPDB-CARE
#3: Sugar ChemComp-NAG / 2-acetamido-2-deoxy-beta-D-glucopyranose / N-acetyl-beta-D-glucosamine / 2-acetamido-2-deoxy-beta-D-glucose / 2-acetamido-2-deoxy-D-glucose / 2-acetamido-2-deoxy-glucose / N-ACETYL-D-GLUCOSAMINE


Type: D-saccharide, beta linking / Mass: 221.208 Da / Num. of mol.: 2 / Source method: isolated from a natural source / Formula: C8H15NO6
IdentifierTypeProgram
DGlcpNAcbCONDENSED IUPAC CARBOHYDRATE SYMBOLGMML 1.0
N-acetyl-b-D-glucopyranosamineCOMMON NAMEGMML 1.0
b-D-GlcpNAcIUPAC CARBOHYDRATE SYMBOLPDB-CARE 1.0
GlcNAcSNFG CARBOHYDRATE SYMBOLGMML 1.0

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Non-polymers , 8 types, 676 molecules

#4: Chemical ChemComp-WSN / N-[(2R)-4-amino-1-imino-4-oxobutan-2-yl]-1-(1-{4-[(2,4-difluorophenyl)methoxy]phenyl}cyclopropane-1-carbonyl)-L-prolinamide


Mass: 498.522 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C26H28F2N4O4
#5: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C2H6O2
#6: Chemical ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#7: Chemical ChemComp-EPE / 4-(2-HYDROXYETHYL)-1-PIPERAZINE ETHANESULFONIC ACID / HEPES


Mass: 238.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18N2O4S / Comment: pH buffer*YM
#8: Chemical ChemComp-FLC / CITRATE ANION


Mass: 189.100 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H5O7
#9: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Mg
#10: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#11: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 664 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 2.01 Å3/Da / Density % sol: 38.88 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 7.8
Details: 25.7mg/mL protein in 25mM HEPES/NaOH pH7, 300 mM NaCl, 200mM Trehalose incubated with 10-fold excess of ligand, then mixed 50-70% with 50-30% reservoir consisting of 20% v/v PEG smear high, ...Details: 25.7mg/mL protein in 25mM HEPES/NaOH pH7, 300 mM NaCl, 200mM Trehalose incubated with 10-fold excess of ligand, then mixed 50-70% with 50-30% reservoir consisting of 20% v/v PEG smear high, 0.15M Li2SO4, 0.05M MgCL2, 0.1M HEPES/NaOH pH 7.8, total volume 200nL

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X10SA / Wavelength: 0.99982 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Mar 23, 2021
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.99982 Å / Relative weight: 1
ReflectionResolution: 1.7→112.62 Å / Num. obs: 128574 / % possible obs: 99 % / Redundancy: 3.02 % / Biso Wilson estimate: 35.81 Å2 / Rmerge(I) obs: 0.076 / Net I/σ(I): 8.32
Reflection shellResolution: 1.7→1.74 Å / Redundancy: 3 % / Rmerge(I) obs: 2.079 / Mean I/σ(I) obs: 0.49 / % possible all: 98.7

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Processing

Software
NameVersionClassificationNB
REFMAC5.8.0267refinement
XSCALEdata scaling
PDB_EXTRACT3.27data extraction
XDSdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: INHOUSE MODEL

Resolution: 1.7→112.62 Å / Cor.coef. Fo:Fc: 0.96 / Cor.coef. Fo:Fc free: 0.944 / SU B: 2.341 / SU ML: 0.072 / Cross valid method: THROUGHOUT / σ(F): 0 / ESU R: 0.119 / ESU R Free: 0.114 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: WITH A MG2+-CITRATE COMPLEX BOUND
RfactorNum. reflection% reflectionSelection details
Rfree0.201 4617 5.1 %RANDOM
Rwork0.169 ---
obs0.171 86420 70.2 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 20.92 Å2
Baniso -1Baniso -2Baniso -3
1--0.07 Å20 Å20.04 Å2
2---0.03 Å20 Å2
3---0.08 Å2
Refinement stepCycle: LAST / Resolution: 1.7→112.62 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6341 0 227 664 7232
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0136922
X-RAY DIFFRACTIONr_bond_other_d0.0010.0176189
X-RAY DIFFRACTIONr_angle_refined_deg1.4431.6679385
X-RAY DIFFRACTIONr_angle_other_deg1.3261.62414303
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.8295812
X-RAY DIFFRACTIONr_dihedral_angle_2_deg36.71923.379364
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.166151112
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.4491527
X-RAY DIFFRACTIONr_chiral_restr0.0730.2872
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.027815
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021604
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it1.241.9563173
X-RAY DIFFRACTIONr_mcbond_other1.2241.9553172
X-RAY DIFFRACTIONr_mcangle_it1.8912.9223962
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.7→1.74 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.281 16 -
Rwork0.27 467 -
obs--5.07 %

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