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- PDB-1zap: SECRETED ASPARTIC PROTEASE FROM C. ALBICANS -

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Basic information

Entry
Database: PDB / ID: 1zap
TitleSECRETED ASPARTIC PROTEASE FROM C. ALBICANS
ComponentsSECRETED ASPARTIC PROTEINASE
KeywordsASPARTIC PROTEASE / SECRETED / CANDIDA ALBICANS
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
Chem-A70 / Secreted aspartic protease 2 / Candidapepsin-2
Similarity search - Component
Biological speciesCandida albicans (yeast)
MethodX-RAY DIFFRACTION / Resolution: 2.5 Å
AuthorsAbad-Zapatero, C. / Muchmore, S.W.
Citation
Journal: Protein Sci. / Year: 1996
Title: Structure of a secreted aspartic protease from C. albicans complexed with a potent inhibitor: implications for the design of antifungal agents.
Authors: Abad-Zapatero, C. / Goldman, R. / Muchmore, S.W. / Hutchins, C. / Stewart, K. / Navaza, J. / Payne, C.D. / Ray, T.L.
#1: Journal: Structure / Year: 1995
Title: The Crystal Structure of a Major Secreted Aspartic Proteinase from Candida Albicans in Complexes with Two Inhibitors
Authors: Cutfield, S.M. / Dodson, E.J. / Anderson, B.F. / Moody, P.C. / Marshall, C.J. / Sullivan, P.A. / Cutfield, J.F.
History
DepositionJan 16, 1996Processing site: BNL
Revision 1.0Apr 21, 1997Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Non-polymer description / Version format compliance
Revision 1.3Jan 18, 2012Group: Non-polymer description
Revision 1.4Oct 30, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Structure summary
Category: chem_comp / chem_comp_atom ...chem_comp / chem_comp_atom / chem_comp_bond / database_2 / entity / pdbx_entity_nonpoly / pdbx_entry_details / pdbx_modification_feature / pdbx_struct_conn_angle / struct_conn / struct_ref_seq_dif / struct_site
Item: _chem_comp.name / _database_2.pdbx_DOI ..._chem_comp.name / _database_2.pdbx_DOI / _database_2.pdbx_database_accession / _entity.pdbx_description / _pdbx_entity_nonpoly.name / _pdbx_entry_details.has_protein_modification / _pdbx_struct_conn_angle.ptnr1_auth_comp_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.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr1_symmetry / _pdbx_struct_conn_angle.ptnr3_auth_comp_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.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.ptnr3_symmetry / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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.ptnr1_symmetry / _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 / _struct_conn.ptnr2_symmetry / _struct_ref_seq_dif.details / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: SECRETED ASPARTIC PROTEINASE
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,1263
Polymers36,3221
Non-polymers8042
Water3,405189
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Unit cell
Length a, b, c (Å)63.600, 98.260, 49.280
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein SECRETED ASPARTIC PROTEINASE / SAP / CANDIDA ALBICANS PROTEASE / CAP


Mass: 36321.602 Da / Num. of mol.: 1 / Source method: isolated from a natural source
Details: CLOSEST ATTC HOMOLOG IS SAP2 ISOLATED FROM C. ALBICANS
Source: (natural) Candida albicans (yeast) / Variant: PATHOGENIC CLINICAL ISOLATE FROM SKIN / Strain: VAL-1 / Tissue: SKIN
References: UniProt: P28871, UniProt: P0CS83*PLUS, candidapepsin
#2: Chemical ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Zn
#3: Chemical ChemComp-A70 / N-ethyl-N-[(4-methylpiperazin-1-yl)carbonyl]-D-phenylalanyl-N-[(1S,2S,4R)-4-(butylcarbamoyl)-1-(cyclohexylmethyl)-2-hyd roxy-5-methylhexyl]-L-norleucinamide / A70450


Mass: 739.042 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C42H70N6O5
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 189 / Source method: isolated from a natural source / Formula: H2O
Compound detailsTHIS ENZYME IS A VERY CLOSE HOMOLOGUE OF THE SECRETED ASPARTIC PROTEASE FROM C. ALBICANS (ATCC ...THIS ENZYME IS A VERY CLOSE HOMOLOGUE OF THE SECRETED ASPARTIC PROTEASE FROM C. ALBICANS (ATCC 10261) REFERRED TO AS SAP2. THE DEPOSITORS REFER TO IT AS SAP2X.
Has protein modificationY

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Experimental details

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Experiment

ExperimentMethod: X-RAY DIFFRACTION

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Sample preparation

CrystalDensity Matthews: 2.12 Å3/Da / Density % sol: 41.96 %
Crystal grow
*PLUS
pH: 4.5 / Method: unknown
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-IDChemical formula
15-10 mg/mlprotein11
225 mMglycine11
325 mM11NaCl
440 mMimidazole/malate12
51 mM12Zn2+
622-24 %PEG800012

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU / Detector: IMAGE PLATE / Date: Jun 1, 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionResolution: 2.5→8 Å / Num. obs: 10193 / % possible obs: 89 % / Observed criterion σ(I): 3.5 / Redundancy: 3 % / Rmerge(I) obs: 0.099
Reflection
*PLUS
Num. measured all: 30743

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Processing

Software
NameVersionClassification
R-AXISdata collection
DENZO(HKL)data reduction
X-PLORmodel building
X-PLORrefinement
R-AXISdata reduction
X-PLORphasing
RefinementResolution: 2.5→8 Å / σ(F): 0 /
RfactorNum. reflection
Rwork0.145 -
obs0.145 10193
Refinement stepCycle: LAST / Resolution: 2.5→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2535 0 54 189 2778
Refine LS restraints
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_bond_d0.009
X-RAY DIFFRACTIONx_bond_d_na
X-RAY DIFFRACTIONx_bond_d_prot
X-RAY DIFFRACTIONx_angle_d
X-RAY DIFFRACTIONx_angle_d_na
X-RAY DIFFRACTIONx_angle_d_prot
X-RAY DIFFRACTIONx_angle_deg1.66
X-RAY DIFFRACTIONx_angle_deg_na
X-RAY DIFFRACTIONx_angle_deg_prot
X-RAY DIFFRACTIONx_dihedral_angle_d
X-RAY DIFFRACTIONx_dihedral_angle_d_na
X-RAY DIFFRACTIONx_dihedral_angle_d_prot
X-RAY DIFFRACTIONx_improper_angle_d
X-RAY DIFFRACTIONx_improper_angle_d_na
X-RAY DIFFRACTIONx_improper_angle_d_prot
X-RAY DIFFRACTIONx_mcbond_it
X-RAY DIFFRACTIONx_mcangle_it
X-RAY DIFFRACTIONx_scbond_it
X-RAY DIFFRACTIONx_scangle_it
Software
*PLUS
Name: X-PLOR / Classification: refinement
Refinement
*PLUS
Solvent computation
*PLUS
Displacement parameters
*PLUS
Refine LS restraints
*PLUS
Refine-IDTypeDev ideal
X-RAY DIFFRACTIONx_dihedral_angle_deg26.78
X-RAY DIFFRACTIONx_improper_angle_deg1.66

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