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- PDB-4awa: Crystal structure of active legumain in complex with YVAD-CMK at ... -

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Basic information

Entry
Database: PDB / ID: 4awa
TitleCrystal structure of active legumain in complex with YVAD-CMK at pH 5.0
Components
  • LEGUMAIN
  • YVAD-CMK
KeywordsHYDROLASE/HYDROLASE INHIBITOR / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / CYSTEINE PROTEASE / LYSOSOMAL / AEP / SUBSTRATE SPECIFICITY / MHCII / ANTIGEN PROCESSING / CANCER
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 / endolysosome lumen / response to acidic pH / positive regulation of monocyte chemotaxis ...negative regulation of ERBB signaling pathway / legumain / vacuolar protein processing / renal system process / Vitamin D (calciferol) metabolism / receptor catabolic process / vitamin D metabolic process / endolysosome lumen / response to acidic pH / positive regulation of monocyte chemotaxis / dendritic spine organization / 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 / endopeptidase activator activity / MHC class II antigen presentation / positive regulation of mitotic cell cycle / lysosomal lumen / cellular response to calcium ion / proteolysis involved in protein catabolic process / protein maturation / positive regulation of long-term synaptic potentiation / antigen processing and presentation of exogenous peptide antigen via MHC class II / tau protein binding / memory / cellular response to amyloid-beta / apical part of cell / late endosome / peptidase activity / negative regulation of neuron apoptotic process / lysosome / negative regulation of gene expression / cysteine-type endopeptidase activity / positive regulation of cell population proliferation / perinuclear region of cytoplasm / proteolysis / extracellular exosome / extracellular region / cytoplasm
Similarity search - Function
Asparaginyl endopeptidase / Legumain prodomain superfamily / : / Legumain, prodomain / Peptidase C13, legumain / Peptidase C13 family / Rossmann fold - #1460 / Rossmann fold / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
ACE-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONE / Legumain
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
SYNTHETIC CONSTRUCT (others)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsDall, E. / Brandstetter, H.
CitationJournal: Proc.Natl.Acad.Sci.USA / Year: 2013
Title: Mechanistic and Structural Studies on Legumain Explain its Zymogenicity, Distinct Activation Pathways, and Regulation
Authors: Dall, E. / Brandstetter, H.
History
DepositionJun 1, 2012Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 26, 2013Provider: repository / Type: Initial release
Revision 1.1Aug 7, 2013Group: Database references
Revision 1.2Oct 23, 2013Group: Other
Revision 1.3Dec 21, 2016Group: Source and taxonomy
Revision 1.4Jul 29, 2020Group: Data collection / Derived calculations ...Data collection / Derived calculations / Other / Structure summary
Category: chem_comp / entity ...chem_comp / entity / pdbx_chem_comp_identifier / pdbx_database_status / pdbx_entity_nonpoly / struct_conn / struct_site / struct_site_gen
Item: _chem_comp.name / _chem_comp.type ..._chem_comp.name / _chem_comp.type / _entity.pdbx_description / _pdbx_database_status.status_code_sf / _pdbx_entity_nonpoly.name / _struct_conn.pdbx_dist_value / _struct_conn.pdbx_leaving_atom_flag / _struct_conn.pdbx_role / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_conn.ptnr2_label_seq_id
Description: Carbohydrate remediation / Provider: repository / Type: Remediation
Revision 1.5Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Refinement description / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _chem_comp.pdbx_synonyms / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.6Nov 13, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature / Item: _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: LEGUMAIN
I: YVAD-CMK
hetero molecules


Theoretical massNumber of molelcules
Total (without water)33,6547
Polymers32,7982
Non-polymers8565
Water2,018112
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area870 Å2
ΔGint-4.2 kcal/mol
Surface area14020 Å2
MethodPISA
Unit cell
Length a, b, c (Å)64.300, 64.300, 79.090
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number77
Space group name H-MP42
Components on special symmetry positions
IDModelComponents
11A-2063-

HOH

21A-2082-

HOH

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Components

#1: Protein LEGUMAIN / ASPARAGINYL ENDOPEPTIDASE / PROTEASE\ / CYSTEINE 1


Mass: 32273.203 Da / Num. of mol.: 1 / Fragment: CATALYTIC DOMAIN, RESIDUES 26-309 / Mutation: YES
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) HOMO SAPIENS (human) / Production host: LEISHMANIA TARENTOLAE (eukaryote) / Strain (production host): P10 / References: UniProt: Q99538, legumain
#2: Protein/peptide YVAD-CMK


Type: Peptide-like / Class: Inhibitor / Mass: 524.996 Da / Num. of mol.: 1 / Source method: obtained synthetically / Source: (synth.) SYNTHETIC CONSTRUCT (others) / References: ACE-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONE
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: SO4
#4: 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.: 3
Source method: isolated from a genetically manipulated 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
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 112 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, ASN 263 TO GLN
Has protein modificationY
Nonpolymer detailsAC-YVAD-CMK (CHAIN I): AC-TYR-VAL-ALA-ASP-CHLOROMETHYLKETONE

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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: 2.49 Å3/Da / Density % sol: 49 % / Description: NONE
Crystal growpH: 5
Details: 0.1 M CITRIC ACID PH 5.0, 0.2 M LITHIUM SULFATE MONOHYDRATE, 25% PEG 3350

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 0.6999
DetectorType: ADSC QUANTUM 315r / Detector: CCD
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.6999 Å / Relative weight: 1
ReflectionResolution: 2.5→64.3 Å / Num. obs: 10650 / % possible obs: 94.9 % / Redundancy: 3.8 % / Rmerge(I) obs: 0.09 / Net I/σ(I): 16.5
Reflection shellResolution: 2.5→7.91 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.23 / Mean I/σ(I) obs: 4 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.6.0117refinement
iMOSFLMdata reduction
SCALAdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4AW9

4aw9


Resolution: 2.5→64.3 Å / Cor.coef. Fo:Fc: 0.902 / Cor.coef. Fo:Fc free: 0.869 / SU B: 10.004 / SU ML: 0.23 / Cross valid method: THROUGHOUT / ESU R: 1.003 / ESU R Free: 0.316 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN USED IF PRESENT IN THE INPUT. U VALUES REFINED INDIVIDUALLY
RfactorNum. reflection% reflectionSelection details
Rfree0.25554 518 4.9 %RANDOM
Rwork0.23739 ---
obs0.23833 10128 94.77 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 32.944 Å2
Baniso -1Baniso -2Baniso -3
1--0.24 Å20 Å20 Å2
2---0.24 Å20 Å2
3---0.47 Å2
Refinement stepCycle: LAST / Resolution: 2.5→64.3 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2151 0 52 112 2315
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0070.022262
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg0.9471.9673072
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg4.2865262
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.99324.545110
X-RAY DIFFRACTIONr_dihedral_angle_3_deg12.69415358
X-RAY DIFFRACTIONr_dihedral_angle_4_deg3.303158
X-RAY DIFFRACTIONr_chiral_restr0.0570.2326
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.0211752
X-RAY DIFFRACTIONr_gen_planes_other
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
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: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.286 33 -
Rwork0.278 756 -
obs--96.34 %

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