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- PDB-3pvk: Secreted aspartic protease 2 in complex with benzamidine -

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Basic information

Entry
Database: PDB / ID: 3pvk
TitleSecreted aspartic protease 2 in complex with benzamidine
ComponentsCandidapepsin-2
KeywordsHYDROLASE
Function / homology
Function and homology information


protein catabolic process => GO:0030163 / : / : / candidapepsin / : / signal peptide processing / protein metabolic process / fungal-type cell wall organization / adhesion of symbiont to host / fungal-type cell wall ...protein catabolic process => GO:0030163 / : / : / candidapepsin / : / signal peptide processing / protein metabolic process / fungal-type cell wall organization / adhesion of symbiont to host / fungal-type cell wall / protein catabolic process / extracellular vesicle / aspartic-type endopeptidase activity / proteolysis / extracellular region / metal ion binding
Similarity search - Function
Secreted aspartic endopeptidase / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily ...Secreted aspartic endopeptidase / Eukaryotic aspartyl protease / Aspartic peptidase A1 family / Peptidase family A1 domain / Peptidase family A1 domain profile. / Cathepsin D, subunit A; domain 1 / Acid Proteases / Aspartic peptidase, active site / Eukaryotic and viral aspartyl proteases active site. / Aspartic peptidase domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
BENZAMIDINE / IMIDAZOLE / Secreted aspartic protease 2 / Candidapepsin-2
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.27 Å
AuthorsKoester, H. / Heine, A. / Klebe, G.
CitationJournal: Chemmedchem / Year: 2012
Title: Experimental and computational active site mapping as a starting point to fragment-based lead discovery.
Authors: Behnen, J. / Koster, H. / Neudert, G. / Craan, T. / Heine, A. / Klebe, G.
History
DepositionDec 7, 2010Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 7, 2011Provider: repository / Type: Initial release
Revision 1.1Jan 18, 2012Group: Database references
Revision 1.2Feb 15, 2012Group: Database references
Revision 2.0Aug 4, 2021Group: Atomic model / Data collection ...Atomic model / Data collection / Derived calculations / Non-polymer description / Structure summary
Category: atom_site / chem_comp ...atom_site / chem_comp / entity / pdbx_entity_nonpoly / pdbx_nonpoly_scheme / pdbx_struct_conn_angle / struct_conn / struct_site / struct_site_gen
Item: _atom_site.B_iso_or_equiv / _atom_site.Cartn_x ..._atom_site.B_iso_or_equiv / _atom_site.Cartn_x / _atom_site.Cartn_y / _atom_site.Cartn_z / _atom_site.auth_comp_id / _atom_site.label_comp_id / _chem_comp.formula / _chem_comp.formula_weight / _chem_comp.id / _entity.formula_weight / _pdbx_entity_nonpoly.comp_id / _pdbx_nonpoly_scheme.mon_id / _pdbx_nonpoly_scheme.pdb_mon_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_site.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id / _struct_site_gen.auth_comp_id / _struct_site_gen.label_comp_id
Revision 2.1Sep 6, 2023Group: 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 2.2Oct 30, 2024Group: Structure summary / Category: pdbx_entry_details / pdbx_modification_feature

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Candidapepsin-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)36,9207
Polymers36,3581
Non-polymers5626
Water5,981332
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)49.380, 63.580, 98.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

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Protein , 1 types, 1 molecules A

#1: Protein Candidapepsin-2 / ACP 2 / Aspartate protease 2 / Secreted aspartic protease 2


Mass: 36357.723 Da / Num. of mol.: 1 / Fragment: UNP residues 57-398 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast)
References: UniProt: P28871, UniProt: P0CS83*PLUS, candidapepsin

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Non-polymers , 5 types, 338 molecules

#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-BEN / BENZAMIDINE


Mass: 120.152 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C7H8N2
#4: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-IMD / IMIDAZOLE


Mass: 69.085 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H5N2
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 332 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 2.12 Å3/Da / Density % sol: 42.1 %
Crystal growTemperature: 289 K / Method: vapor diffusion, sitting drop / pH: 6.5
Details: 9 mM ZnAc, 16% PEG 8000, 0.1M imidazole/malate buffer pH 6.5, VAPOR DIFFUSION, SITTING DROP, temperature 289K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: SLS / Beamline: X06DA / Wavelength: 1 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jul 31, 2009 / Details: mirrors
RadiationMonochromator: Bertels Monochromator with dual channel cut crystals (DCCM) in (+--+) geometry
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 1.27→40 Å / Num. all: 79920 / Num. obs: 79920 / % possible obs: 100 % / Redundancy: 6.8 % / Rsym value: 0.071 / Net I/σ(I): 26.2
Reflection shellResolution: 1.27→1.29 Å / Redundancy: 3.7 % / Mean I/σ(I) obs: 2.9 / Num. unique all: 3341 / Rsym value: 0.418 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
PHENIX(phenix.refine: 1.6.4_486)refinement
HKL-2000data reduction
HKL-2000data scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1EAG

1eag


Resolution: 1.27→38.999 Å / SU ML: 0.12 / σ(F): 0 / Stereochemistry target values: ML
RfactorNum. reflection% reflectionSelection details
Rfree0.1841 3895 5.05 %RANDOM
Rwork0.1679 ---
obs0.1687 77092 93.61 %-
all-77092 --
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL / Bsol: 39.22 Å2 / ksol: 0.358 e/Å3
Displacement parameters
Baniso -1Baniso -2Baniso -3
1--0.8935 Å20 Å2-0 Å2
2--2.0273 Å20 Å2
3----1.1338 Å2
Refinement stepCycle: LAST / Resolution: 1.27→38.999 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2404 0 37 332 2773
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0052560
X-RAY DIFFRACTIONf_angle_d1.063504
X-RAY DIFFRACTIONf_dihedral_angle_d12.415889
X-RAY DIFFRACTIONf_chiral_restr0.072418
X-RAY DIFFRACTIONf_plane_restr0.004463
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
1.2702-1.31560.21732940.21736140X-RAY DIFFRACTION80
1.3156-1.36830.19513850.18786903X-RAY DIFFRACTION89
1.3683-1.43060.1833900.17276981X-RAY DIFFRACTION91
1.4306-1.5060.18563830.16557161X-RAY DIFFRACTION93
1.506-1.60040.17273920.15757320X-RAY DIFFRACTION94
1.6004-1.72390.18543940.15827422X-RAY DIFFRACTION95
1.7239-1.89740.17354110.1557578X-RAY DIFFRACTION97
1.8974-2.1720.17864150.15547682X-RAY DIFFRACTION98
2.172-2.73630.18164170.16817848X-RAY DIFFRACTION99
2.7363-39.01770.18864140.17338162X-RAY DIFFRACTION100

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