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- PDB-1eag: Secreted aspartic proteinase (SAP2) from Candida albicans complex... -

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Basic information

Entry
Database: PDB / ID: 1eag
TitleSecreted aspartic proteinase (SAP2) from Candida albicans complexed with A70450
ComponentsASPARTIC PROTEINASE (SAP2 GENE PRODUCT)
KeywordsHYDROLASE/HYDROLASE INHIBITOR / SAP2 / CANDIDA ALBICANS / HYDROLASE-HYDROLASE INHIBITOR COMPLEX / ASPARTIC PROTEASE
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: 2.1 Å
AuthorsCutfield, J.F. / Cutfield, S.M.
Citation
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.E. / Marshall, C.J. / Sullivan, P.A. / Cutfield, J.F.
#1: Journal: J.Mol.Biol. / Year: 1993
Title: Crystallization of Inhibited Aspartic Proteinase from Candida Albicans
Authors: Cutfield, S. / Marshall, C. / Moody, P. / Sullivan, P. / Cutfield, J.
History
DepositionMay 31, 1996Processing site: BNL
Revision 1.0Dec 23, 1996Provider: repository / Type: Initial release
Revision 1.1Mar 24, 2008Group: Version format compliance
Revision 1.2Jul 13, 2011Group: Atomic model / Database references ...Atomic model / Database references / Derived calculations / Non-polymer description / Structure summary / 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 / 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 / _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: ASPARTIC PROTEINASE (SAP2 GENE PRODUCT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)37,0972
Polymers36,3581
Non-polymers7391
Water2,144119
1
A: ASPARTIC PROTEINASE (SAP2 GENE PRODUCT)
hetero molecules

A: ASPARTIC PROTEINASE (SAP2 GENE PRODUCT)
hetero molecules


Theoretical massNumber of molelcules
Total (without water)74,1944
Polymers72,7152
Non-polymers1,4782
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation8_665-y+1,-x+1,-z+1/21
Unit cell
Length a, b, c (Å)76.200, 76.200, 126.100
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number96
Space group name H-MP43212

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Components

#1: Protein ASPARTIC PROTEINASE (SAP2 GENE PRODUCT) / SAP2 / CANDIDAPEPSIN


Mass: 36357.723 Da / Num. of mol.: 1 / Source method: isolated from a natural source / Source: (natural) Candida albicans (yeast)
References: UniProt: P28871, UniProt: P0CS83*PLUS, candidapepsin
#2: 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
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 119 / Source method: isolated from a natural source / Formula: H2O
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: 2.52 Å3/Da / Density % sol: 50 %
Crystal grow
*PLUS
Temperature: 20 ℃ / pH: 6.2 / Method: vapor diffusion, hanging drop / Details: Cutfield, S., (1993) J.Mol.Biol., 234, 1266.
Components of the solutions
*PLUS
IDConc.Common nameCrystal-IDSol-ID
110 mg/mlprotein1drop
22.2 Mammonium sulfate1reservoir
30.5 Msodium chloride1reservoir
420 mMTris-HCl1reservoir
550 mMsodium citrate1reservoir

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Data collection

Diffraction sourceWavelength: 1.5418
DetectorType: RIGAKU RAXIS IIC / Detector: IMAGE PLATE / Date: 1993
RadiationMonochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.5418 Å / Relative weight: 1
ReflectionNum. obs: 24302 / % possible obs: 98 % / Redundancy: 7.5 % / Rmerge(I) obs: 0.072
Reflection
*PLUS
Highest resolution: 2.05 Å

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Processing

Software
NameClassification
DENZOdata reduction
PROLSQrefinement
RefinementResolution: 2.1→8 Å / σ(F): 0
Details: LOOP RESIDUES A 284, A 285, AND A 286 HAVE WEAK, DISORDERED DENSITY AND THEIR COORDINATES HAVE BEEN OMITTED.
RfactorNum. reflection% reflection
Rfree0.268 -5 %
Rwork0.195 --
all-21780 -
obs-21780 -
Displacement parametersBiso mean: 32.4 Å2
Refinement stepCycle: LAST / Resolution: 2.1→8 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms2538 0 53 119 2710
Refine LS restraints
Refine-IDTypeDev idealDev ideal target
X-RAY DIFFRACTIONp_bond_d0.010.02
X-RAY DIFFRACTIONp_angle_d0.0350.04
X-RAY DIFFRACTIONp_angle_deg
X-RAY DIFFRACTIONp_planar_d0.0330.05
X-RAY DIFFRACTIONp_hb_or_metal_coord
X-RAY DIFFRACTIONp_mcbond_it0.971.5
X-RAY DIFFRACTIONp_mcangle_it1.722
X-RAY DIFFRACTIONp_scbond_it1.492
X-RAY DIFFRACTIONp_scangle_it2.452.5
X-RAY DIFFRACTIONp_plane_restr0.0110.02
X-RAY DIFFRACTIONp_chiral_restr0.0950.12
X-RAY DIFFRACTIONp_singtor_nbd0.2050.5
X-RAY DIFFRACTIONp_multtor_nbd0.2780.5
X-RAY DIFFRACTIONp_xhyhbond_nbd
X-RAY DIFFRACTIONp_xyhbond_nbd0.1770.5
X-RAY DIFFRACTIONp_planar_tor1.8753
X-RAY DIFFRACTIONp_staggered_tor18.315
X-RAY DIFFRACTIONp_orthonormal_tor
X-RAY DIFFRACTIONp_transverse_tor17.320
X-RAY DIFFRACTIONp_special_tor
Software
*PLUS
Name: PROLSQ / Classification: refinement
Refinement
*PLUS
Rfactor obs: 0.195
Solvent computation
*PLUS
Displacement parameters
*PLUS

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