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- PDB-6r61: Major aspartyl peptidase 1 from C. neoformans in complex with Inh... -

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Basic information

Entry
Database: PDB / ID: 6r61
TitleMajor aspartyl peptidase 1 from C. neoformans in complex with Inhibitor LP258
ComponentsMajor aspartyl peptidase 1
KeywordsHYDROLASE / aspartyl protease / secreted / Cryptococcus neoformans / inhibitor complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases / aspartic-type endopeptidase activity / proteolysis / extracellular region
Similarity search - Function
Pepsin-like domain / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Aspartic peptidase domain superfamily
Similarity search - Domain/homology
: / DI(HYDROXYETHYL)ETHER / TRIETHYLENE GLYCOL / Major aspartyl peptidase 1
Similarity search - Component
Biological speciesCryptococcus neoformans (Cryptococcus neoformans serotype A)
MethodX-RAY DIFFRACTION / FOURIER SYNTHESIS / Resolution: 1.81 Å
AuthorsKrystufek, R. / Sacha, P. / Brynda, J. / Konvalinka, J.
Funding support Czech Republic, 1items
OrganizationGrant numberCountry
Ministry of Education (MoE, Czech Republic)InterBioMed LO1302 Czech Republic
CitationJournal: To Be Published
Title: Major aspartyl peptidase 1 from C. neoformans in complex with Inhibitor LP258
Authors: Krystufek, R. / Sacha, P. / Brynda, J. / Konvalinka, J.
History
DepositionMar 26, 2019Deposition site: PDBE / Processing site: PDBE
Revision 1.0Apr 7, 2021Provider: repository / Type: Initial release
Revision 1.1Jan 24, 2024Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Nov 6, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature
Revision 2.0Mar 26, 2025Group: Advisory / Atomic model ...Advisory / Atomic model / Author supporting evidence / Data collection / Database references / Derived calculations / Non-polymer description / Other / Polymer sequence / Refinement description / Source and taxonomy / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / chem_comp_atom / chem_comp_bond / diffrn_radiation_wavelength / diffrn_source / entity / entity_name_com / entity_poly / entity_poly_seq / entity_src_gen / pdbx_audit_support / pdbx_branch_scheme / pdbx_contact_author / pdbx_database_status / pdbx_entity_branch_descriptor / pdbx_entity_instance_feature / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_nonpoly_scheme / pdbx_poly_seq_scheme / pdbx_struct_assembly_prop / pdbx_struct_conn_angle / pdbx_struct_sheet_hbond / pdbx_struct_special_symmetry / pdbx_unobs_or_zero_occ_atoms / pdbx_unobs_or_zero_occ_residues / pdbx_validate_torsion / refine / refine_hist / refine_ls_restr / refine_ls_shell / software / struct_asym / struct_conf / struct_conn / struct_mon_prot_cis / struct_ref / struct_ref_seq / struct_ref_seq_dif / struct_sheet_range
Item: _chem_comp.formula / _chem_comp.formula_weight ..._chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _chem_comp.mon_nstd_flag / _chem_comp.name / _chem_comp.pdbx_synonyms / _chem_comp.type / _diffrn_radiation_wavelength.wavelength / _diffrn_source.pdbx_wavelength_list / _entity_poly.pdbx_seq_one_letter_code / _entity_poly.pdbx_seq_one_letter_code_can / _entity_src_gen.pdbx_end_seq_num / _entity_src_gen.pdbx_gene_src_gene / _pdbx_audit_support.funding_organization / _pdbx_branch_scheme.auth_asym_id / _pdbx_branch_scheme.auth_seq_num / _pdbx_contact_author.id / _pdbx_database_status.pdb_format_compatible / _pdbx_entity_branch_descriptor.descriptor / _pdbx_entry_details.has_ligand_of_interest / _pdbx_modification_feature.label_seq_id / _pdbx_modification_feature.modified_residue_label_seq_id / _pdbx_nonpoly_scheme.auth_mon_id / _pdbx_nonpoly_scheme.auth_seq_num / _pdbx_nonpoly_scheme.entity_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_nonpoly_scheme.pdb_seq_num / _pdbx_struct_assembly_prop.value / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr2_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _pdbx_struct_sheet_hbond.range_1_auth_comp_id / _pdbx_struct_sheet_hbond.range_1_auth_seq_id / _pdbx_struct_sheet_hbond.range_1_label_comp_id / _pdbx_struct_sheet_hbond.range_1_label_seq_id / _pdbx_struct_sheet_hbond.range_2_auth_comp_id / _pdbx_struct_sheet_hbond.range_2_auth_seq_id / _pdbx_struct_sheet_hbond.range_2_label_comp_id / _pdbx_struct_sheet_hbond.range_2_label_seq_id / _pdbx_struct_special_symmetry.auth_seq_id / _pdbx_validate_torsion.phi / _pdbx_validate_torsion.psi / _refine.B_iso_max / _refine.B_iso_mean / _refine.B_iso_min / _refine.aniso_B[1][1] / _refine.aniso_B[2][2] / _refine.aniso_B[3][3] / _refine.correlation_coeff_Fo_to_Fc_free / _refine.details / _refine.ls_R_factor_R_free / _refine.ls_R_factor_R_work / _refine.ls_R_factor_obs / _refine.ls_d_res_low / _refine.overall_SU_B / _refine.overall_SU_ML / _refine.overall_SU_R_Cruickshank_DPI / _refine.pdbx_ls_sigma_F / _refine.pdbx_overall_ESU_R / _refine.pdbx_overall_ESU_R_Free / _refine.pdbx_stereochemistry_target_values / _refine.solvent_model_details / _refine_hist.cycle_id / _refine_hist.d_res_low / _refine_hist.number_atoms_solvent / _refine_hist.number_atoms_total / _refine_hist.pdbx_B_iso_mean_ligand / _refine_hist.pdbx_B_iso_mean_solvent / _refine_hist.pdbx_number_residues_total / _refine_ls_shell.R_factor_R_free / _refine_ls_shell.R_factor_R_free_error / _refine_ls_shell.R_factor_R_work / _refine_ls_shell.number_reflns_all / _struct_asym.entity_id / _struct_conf.beg_label_seq_id / _struct_conf.end_auth_comp_id / _struct_conf.end_auth_seq_id / _struct_conf.end_label_comp_id / _struct_conf.end_label_seq_id / _struct_conf.pdbx_PDB_helix_length / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_seq_id / _struct_mon_prot_cis.label_seq_id / _struct_mon_prot_cis.pdbx_label_seq_id_2 / _struct_mon_prot_cis.pdbx_omega_angle / _struct_ref.db_code / _struct_ref.pdbx_align_begin / _struct_ref.pdbx_seq_one_letter_code / _struct_ref_seq.db_align_beg / _struct_ref_seq.db_align_end / _struct_ref_seq.pdbx_auth_seq_align_beg / _struct_ref_seq.pdbx_auth_seq_align_end / _struct_ref_seq.seq_align_end / _struct_sheet_range.beg_auth_comp_id / _struct_sheet_range.beg_auth_seq_id / _struct_sheet_range.beg_label_comp_id / _struct_sheet_range.beg_label_seq_id / _struct_sheet_range.end_label_seq_id
Description: Ligand geometry
Details: We had to correct the position of the nitrogen atom in heterocycl.
Provider: author / Type: Coordinate replacement

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Major aspartyl peptidase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)48,95913
Polymers46,7641
Non-polymers2,19512
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2650 Å2
ΔGint-3 kcal/mol
Surface area14490 Å2
MethodPISA
Unit cell
Length a, b, c (Å)97.170, 113.390, 91.220
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221
Components on special symmetry positions
IDModelComponents
11A-529-

HOH

21A-665-

HOH

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Components

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Protein / Sugars , 2 types, 2 molecules A

#1: Protein Major aspartyl peptidase 1 / Aspartic protease / Aspartyl endopeptidase May1 / Endopeptidase


Mass: 46764.352 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Details: MayI(17-434)-Avitag
Source: (gene. exp.) Cryptococcus neoformans (Cryptococcus neoformans serotype A)
Gene: cnap1, MAY1, CNAG_05872 / Plasmid: pMT_BIP_MayI(17-434)Avitag / Production host: Drosophila melanogaster (fruit fly) / Variant (production host): Schneider S2
References: UniProt: J9VS02, Hydrolases; Acting on peptide bonds (peptidases); Aspartic endopeptidases
#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-ROHGlycam 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
[][D-1-deoxy-GlcpNAc]{[(4+1)][b-D-GlcpNAc]{}}LINUCSPDB-CARE

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Non-polymers , 8 types, 202 molecules

#3: Chemical
ChemComp-PEG / DI(HYDROXYETHYL)ETHER


Mass: 106.120 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C4H10O3
#4: Chemical ChemComp-PGE / TRIETHYLENE GLYCOL


Mass: 150.173 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O4
#5: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: SO4
#6: Chemical ChemComp-1PE / PENTAETHYLENE GLYCOL / PEG400


Mass: 238.278 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C10H22O6 / Comment: precipitant*YM
#7: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Cl
#8: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#9: Chemical ChemComp-A1IY5 / (3~{S},7~{S},8~{S})-7-oxidanyl-8-(phenylmethyl)-3-(pyridin-3-ylmethyl)-1,4,9-triazacyclotricosane-2,5,10-trione


Mass: 564.759 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Formula: C33H48N4O4 / Feature type: SUBJECT OF INVESTIGATION
#10: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestY
Has protein modificationY

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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: 3.41 Å3/Da / Density % sol: 63.96 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop
Details: peptidase (85 mg/ml) in 50 mM sodium acetate, pH=5.0, 100mM NaCl in equal volume with reservoir solution: 100mM lithium sulphate, 45% (v/v) PEG-400, 100 mM sodium acetate pH= 4.5
PH range: 4.5 - 5.0

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: ROTATING ANODE / Type: RIGAKU MICROMAX-007 HF / Wavelength: 1.54187 Å
DetectorType: DECTRIS PILATUS 300K / Detector: PIXEL / Date: Sep 11, 2018
RadiationMonochromator: Confocal Max-Flux optics Rigaku / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.54187 Å / Relative weight: 1
ReflectionResolution: 1.81→73.78 Å / Num. obs: 44101 / % possible obs: 95.8 % / Redundancy: 3.764 % / Biso Wilson estimate: 24.145 Å2 / CC1/2: 0.991 / Rmerge(I) obs: 0.175 / Rrim(I) all: 0.202 / Χ2: 0.892 / Net I/σ(I): 6.66
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.81-1.863.651.5250.8828490.3571.76984.5
1.86-1.913.7851.1351.2229910.5441.31291.1
1.91-1.973.8710.9031.6229860.6011.04193
1.97-2.033.8920.6292.3229750.7610.72395.7
2.03-2.093.9590.4952.9728760.8090.56897.4
2.09-2.173.980.3923.6928490.8840.44997.2
2.17-2.253.9810.3474.1927430.9060.39897.7
2.25-2.343.9630.3054.5926570.9170.3597.4
2.34-2.443.950.2715.125330.9370.31297.8
2.44-2.563.8960.2375.5324670.9590.27398
2.56-2.73.8160.2096.1523310.9610.24298.5
2.7-2.873.7260.177.1922410.9690.19799.2
2.87-3.063.5890.1279.1220910.9820.14999.6
3.06-3.313.3210.09711.2919610.9880.11599.4
3.31-3.622.7560.06813.4417850.9910.08497.1
3.62-4.052.9480.05616.5814880.9950.06788.9
4.05-4.683.8330.0520.7914580.9970.05899.7
4.68-5.734.0830.05519.7612580.9970.06499.5
5.73-8.114.0010.06517.319920.9970.07599.6
8.11-73.783.6470.0424.425700.9980.04797.8

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Processing

Software
NameVersionClassification
REFMAC5.8.0267refinement
XDSdata reduction
XSCALEdata scaling
PDB_EXTRACT3.24data extraction
MOLREPphasing
RefinementMethod to determine structure: FOURIER SYNTHESIS
Starting model: 6R5H

6r5h


Resolution: 1.81→45.65 Å / Cor.coef. Fo:Fc: 0.956 / Cor.coef. Fo:Fc free: 0.95 / SU B: 4.815 / SU ML: 0.149 / Cross valid method: THROUGHOUT / ESU R: 0.108 / ESU R Free: 0.1 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20361 2240 5 %RANDOM
Rwork0.18631 ---
obs0.18719 42553 96.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 32.828 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2--0.01 Å20 Å2
3----0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.81→45.65 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2582 0 134 191 2907
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0130.0132838
X-RAY DIFFRACTIONr_bond_other_d0.0020.0182534
X-RAY DIFFRACTIONr_angle_refined_deg1.7171.6653858
X-RAY DIFFRACTIONr_angle_other_deg1.51.6055885
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6535374
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.64924.035114
X-RAY DIFFRACTIONr_dihedral_angle_3_deg11.67415408
X-RAY DIFFRACTIONr_dihedral_angle_4_deg19.017157
X-RAY DIFFRACTIONr_chiral_restr0.0810.2393
X-RAY DIFFRACTIONr_gen_planes_refined0.010.023250
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02649
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_it2.5293.2821425
X-RAY DIFFRACTIONr_mcbond_other2.5283.2821426
X-RAY DIFFRACTIONr_mcangle_it3.0434.9041786
X-RAY DIFFRACTIONr_mcangle_other3.0434.9061787
X-RAY DIFFRACTIONr_scbond_it4.3553.7061412
X-RAY DIFFRACTIONr_scbond_other4.3543.7051413
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.6355.3932059
X-RAY DIFFRACTIONr_long_range_B_refined6.49439.7273100
X-RAY DIFFRACTIONr_long_range_B_other6.49339.7213101
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.81→1.857 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.384 145 -
Rwork0.371 2726 -
obs--85.19 %

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