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- PDB-3qvi: Crystal structure of KNI-10395 bound histo-aspartic protease (HAP... -

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Basic information

Entry
Database: PDB / ID: 3qvi
TitleCrystal structure of KNI-10395 bound histo-aspartic protease (HAP) from Plasmodium falciparum
ComponentsHisto-aspartic protease
KeywordsHYDROLASE/HYDROLASE INHIBITOR / Histo-aspartic protease / HAP / Plasmepsin / Aspartic protease / Malaria / KNI / KNI-10395 / HYDROLASE-HYDROLASE INHIBITOR complex
Function / homology
Function and homology information


plasmepsin II / acquisition of nutrients from host / vacuolar lumen / food vacuole / aspartic-type endopeptidase activity / proteolysis / membrane
Similarity search - Function
Pepsin-like domain / 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 domain superfamily / Beta Barrel / Mainly Beta
Similarity search - Domain/homology
KNI-10395 / ACETATE ION / Chem-K95 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE / Plasmepsin III
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsBhaumik, P. / Gustchina, A. / Wlodawer, A.
CitationJournal: Biochemistry / Year: 2011
Title: Structural insights into the activation and inhibition of histo-aspartic protease from Plasmodium falciparum.
Authors: Bhaumik, P. / Xiao, H. / Hidaka, K. / Gustchina, A. / Kiso, Y. / Yada, R.Y. / Wlodawer, A.
History
DepositionFeb 25, 2011Deposition site: RCSB / Processing site: RCSB
Revision 1.0Oct 12, 2011Provider: repository / Type: Initial release
Revision 1.1Nov 30, 2011Group: Database references
Revision 1.2Dec 12, 2012Group: Other
Revision 1.3Sep 4, 2013Group: Other
Revision 1.4Nov 27, 2024Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description / 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_conn / struct_ncs_dom_lim / 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_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.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_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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

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Assembly

Deposited unit
A: Histo-aspartic protease
B: Histo-aspartic protease
C: Histo-aspartic protease
D: Histo-aspartic protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)210,91726
Polymers207,0204
Non-polymers3,89722
Water9,152508
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Histo-aspartic protease
B: Histo-aspartic protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,28312
Polymers103,5102
Non-polymers1,77310
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9860 Å2
ΔGint-44 kcal/mol
Surface area26560 Å2
MethodPISA
3
C: Histo-aspartic protease
D: Histo-aspartic protease
hetero molecules


Theoretical massNumber of molelcules
Total (without water)105,63414
Polymers103,5102
Non-polymers2,12412
Water362
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10130 Å2
ΔGint-40 kcal/mol
Surface area25830 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.430, 90.510, 192.410
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B
12C
22D

NCS domain segments:

Refine code: 4

Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111GLUGLULEULEUAA0 - 73125 - 198
211GLUGLULEULEUBB0 - 73125 - 198
121SERSERLEULEUAA81 - 155206 - 281
221SERSERLEULEUBB81 - 155206 - 281
131TYRTYRPHEPHEAA164 - 228290 - 350
231TYRTYRPHEPHEBB164 - 228290 - 350
141LEULEULEULEUAA255 - 278377 - 400
241LEULEULEULEUBB255 - 278377 - 400
151LEULEUASNASNAA281 - 327407 - 450
251LEULEUASNASNBB281 - 327407 - 450
112GLUGLULEULEUCC0 - 73125 - 198
212GLUGLULEULEUDD0 - 73125 - 198
122SERSERLEULEUCC81 - 155206 - 281
222SERSERLEULEUDD81 - 155206 - 281
132TYRTYRPHEPHECC164 - 228290 - 350
232TYRTYRPHEPHEDD164 - 228290 - 350
142LEULEULEULEUCC255 - 278377 - 400
242LEULEULEULEUDD255 - 278377 - 400
152LEULEUASNASNCC281 - 327407 - 450
252LEULEUASNASNDD281 - 327407 - 450

NCS ensembles :
ID
1
2

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Components

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Protein , 1 types, 4 molecules ABCD

#1: Protein
Histo-aspartic protease / HAP protein / Putative aspartic proteinase


Mass: 51754.973 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Plasmodium falciparum (malaria parasite P. falciparum)
Gene: hap / Plasmid: pET32b(+) / Production host: Escherichia coli (E. coli) / Strain (production host): Rosetta-gami B (DE3) pLysS / References: UniProt: Q9Y006

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Non-polymers , 7 types, 530 molecules

#2: Chemical ChemComp-K95 / (4R)-N-[(1S,2R)-2-hydroxy-2,3-dihydro-1H-inden-1-yl]-3-[(2S,3S)-2-hydroxy-3-{[S-methyl-N-(phenylacetyl)-L-cysteinyl]ami no}-4-phenylbutanoyl]-5,5-dimethyl-1,3-thiazolidine-4-carboxamide / KNI-10395


Type: peptide-like, Peptide-like / Class: Inhibitor / Mass: 704.898 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C37H44N4O6S2 / References: KNI-10395
#3: Chemical
ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 12 / Source method: obtained synthetically / Formula: C2H6O2
#4: Chemical
ChemComp-PG4 / TETRAETHYLENE GLYCOL


Mass: 194.226 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C8H18O5 / Comment: precipitant*YM
#5: Chemical ChemComp-ACT / ACETATE ION


Mass: 59.044 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H3O2
#6: Chemical ChemComp-PG5 / 1-METHOXY-2-[2-(2-METHOXY-ETHOXY]-ETHANE


Mass: 178.226 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C8H18O4
#7: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: Na
#8: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 508 / 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: 1.86 Å3/Da / Density % sol: 33.86 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 4.5
Details: 30% (v/v) PEG 200, 0.1M Sodium Chloride, 0.1M Sodium acetate, pH 4.5, VAPOR DIFFUSION, SITTING DROP, temperature 293K

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 22-ID / Wavelength: 1 Å
DetectorType: MAR scanner 300 mm plate / Detector: IMAGE PLATE / Date: Aug 9, 2010
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1 Å / Relative weight: 1
ReflectionResolution: 2.2→40 Å / Num. all: 79116 / Num. obs: 79116 / % possible obs: 100 % / Redundancy: 6 % / Rmerge(I) obs: 0.209 / Net I/σ(I): 9.4
Reflection shellResolution: 2.2→2.3 Å / Redundancy: 7.3 % / Rmerge(I) obs: 0.1902 / Mean I/σ(I) obs: 1.05 / % possible all: 100

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Processing

Software
NameVersionClassification
MAR345dtbdata collection
PHASERphasing
REFMAC5.5.0104refinement
XDSdata reduction
XDSdata scaling
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→39.72 Å / Cor.coef. Fo:Fc: 0.953 / Cor.coef. Fo:Fc free: 0.907 / SU B: 20.656 / SU ML: 0.211 / Cross valid method: THROUGHOUT / ESU R: 0.606 / ESU R Free: 0.301 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.25187 2712 5 %RANDOM
Rwork0.17503 ---
obs0.17882 51509 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 39.922 Å2
Baniso -1Baniso -2Baniso -3
1--0.12 Å20 Å20 Å2
2--0.4 Å20 Å2
3----0.28 Å2
Refinement stepCycle: LAST / Resolution: 2.5→39.72 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms10393 0 255 508 11156
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.02211063
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.931.98215021
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.36651351
X-RAY DIFFRACTIONr_dihedral_angle_2_deg38.11925.644489
X-RAY DIFFRACTIONr_dihedral_angle_3_deg21.063151867
X-RAY DIFFRACTIONr_dihedral_angle_4_deg25.7921512
X-RAY DIFFRACTIONr_chiral_restr0.1490.21667
X-RAY DIFFRACTIONr_gen_planes_refined0.0080.0218318
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_it0.7691.56607
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it1.478210804
X-RAY DIFFRACTIONr_scbond_it2.30134456
X-RAY DIFFRACTIONr_scangle_it3.8084.54192
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
Rfree0.338 198 -
Rwork0.245 3750 -
obs--100 %
Refinement TLS params.

Method: refined / Refine-ID: X-RAY DIFFRACTION

IDL11 (°2)L12 (°2)L13 (°2)L22 (°2)L23 (°2)L33 (°2)S11 (Å °)S12 (Å °)S13 (Å °)S21 (Å °)S22 (Å °)S23 (Å °)S31 (Å °)S32 (Å °)S33 (Å °)T11 (Å2)T12 (Å2)T13 (Å2)T22 (Å2)T23 (Å2)T33 (Å2)Origin x (Å)Origin y (Å)Origin z (Å)
12.16060.27480.04771.28140.27032.4821-0.0438-0.1140.23370.10480.02360.0498-0.1973-0.35510.02030.05950.04530.02930.1718-0.02050.06581.349-7.1617.825
23.2871-1.2961-0.27831.6583-0.13462.2603-0.00140.3040.26980.0473-0.0441-0.1499-0.06230.15270.04550.1128-0.0398-0.00580.15460.03270.049717.428-12.281-11.003
31.6292-0.05360.50890.81150.04212.83850.00240.11290.1360.01320.0225-0.0693-0.22480.4158-0.02480.1007-0.0272-0.00390.20380.02550.068521.079-9.08-11.333
43.49361.55830.50621.11090.36880.172-0.20640.3040.4452-0.47570.10550.242-0.34860.02650.1011.1283-0.0845-0.22140.31690.1320.303829.95822.242-5.14
50.9688-0.40520.45572.88190.4062.2477-0.23110.1930.2378-0.43240.1120.011-0.82390.38490.11910.4849-0.1564-0.07540.26650.00350.168836.66611.7627.439
61.66580.64241.42011.23970.85252.5854-0.1520.09080.1102-0.17990.10710.0215-0.32720.2860.04490.1558-0.03-0.00780.1753-0.0130.054633.729-1.68412.722
72.2283-0.92310.20021.74360.74781.2699-0.02130.1173-0.1177-0.0651-0.03660.0655-0.1187-0.2460.0580.07290.0444-0.02050.29-0.0670.06062.58110.65740.709
84.48731.10620.23021.22360.52663.37610.0042-0.2281-0.21370.0102-0.0355-0.0362-0.1333-0.19370.03120.09110.02660.00840.17470.0180.040115.05513.1159.895
90.9094-0.56050.14131.2710.70292.0597-0.009-0.0865-0.0432-0.00350.0804-0.1259-0.0630.1315-0.07140.0966-0.00020.01210.2047-0.02320.070723.4229.60460.061
101.8422-0.387-0.22472.5124-0.67421.25770.0281-0.1536-0.04370.0790.00180.057-0.0484-0.1314-0.030.0185-0.0084-0.01690.14410.01630.058327.342-23.10652.999
111.72281.1417-0.12892.7847-0.11161.0302-0.07110.01820.0001-0.16510.0634-0.00860.0687-0.03440.00760.08170.0234-0.01550.1861-0.02950.026335.521-8.56835.948
120.9408-0.037-0.4511.4983-0.07280.99590.0138-0.06010.0725-0.02960.0336-0.0679-0.04690.0441-0.04740.06770.0002-0.01830.1698-0.02290.021233.6810.04336.45
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 149
2X-RAY DIFFRACTION2A150 - 245
3X-RAY DIFFRACTION3A246 - 327
4X-RAY DIFFRACTION4B0 - 95
5X-RAY DIFFRACTION5B96 - 237
6X-RAY DIFFRACTION6B238 - 327
7X-RAY DIFFRACTION7C0 - 149
8X-RAY DIFFRACTION8C150 - 230
9X-RAY DIFFRACTION9C231 - 327
10X-RAY DIFFRACTION10D0 - 148
11X-RAY DIFFRACTION11D149 - 235
12X-RAY DIFFRACTION12D236 - 327

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