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- PDB-3bwk: Crystal Structure of Falcipain-3 with Its inhibitor, K11017 -

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Basic information

Entry
Database: PDB / ID: 3bwk
TitleCrystal Structure of Falcipain-3 with Its inhibitor, K11017
ComponentsCysteine protease falcipain-3
KeywordsHYDROLASE / falcipain / malaria / cysteine protease
Function / homology
Function and homology information


membrane-bounded organelle / cysteine-type peptidase activity / proteolysis / membrane
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease / Cysteine proteinases / Cysteine peptidase, cysteine active site / Eukaryotic thiol (cysteine) proteases cysteine active site. / Cathepsin B; Chain A / Papain-like cysteine peptidase superfamily / Alpha-Beta Complex / Alpha Beta
Similarity search - Domain/homology
Chem-C1P / Cysteine protease falcipain-3 / Cysteine protease falcipain-3
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.42 Å
AuthorsKerr, I. / Lee, J.H. / Brinen, L.S.
CitationJournal: J.Biol.Chem. / Year: 2009
Title: Vinyl sulfones as antiparasitic agents and a structural basis for drug design.
Authors: Kerr, I.D. / Lee, J.H. / Farady, C.J. / Marion, R. / Rickert, M. / Sajid, M. / Pandey, K.C. / Caffrey, C.R. / Legac, J. / Hansell, E. / McKerrow, J.H. / Craik, C.S. / Rosenthal, P.J. / Brinen, L.S.
History
DepositionJan 9, 2008Deposition site: RCSB / Processing site: RCSB
Revision 1.0Jan 20, 2009Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Version format compliance
Revision 1.2Sep 7, 2011Group: Non-polymer description
Revision 1.3Aug 30, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_conn.pdbx_leaving_atom_flag / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id
Revision 1.4Nov 20, 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: Cysteine protease falcipain-3
B: Cysteine protease falcipain-3
C: Cysteine protease falcipain-3
D: Cysteine protease falcipain-3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)112,10113
Polymers109,5024
Non-polymers2,5999
Water8,953497
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area9910 Å2
ΔGint-101 kcal/mol
Surface area39360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)113.996, 113.996, 226.116
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number92
Space group name H-MP41212

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Components

#1: Protein
Cysteine protease falcipain-3


Mass: 27375.580 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q9NBA7, UniProt: Q9NAW4*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-C1P / N~2~-(morpholin-4-ylcarbonyl)-N-[(3S)-1-phenyl-5-(phenylsulfonyl)pentan-3-yl]-L-leucinamide / K11017, bound form


Mass: 529.691 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C28H39N3O5S
#3: Chemical
ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 5 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 497 / 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 / Number of used crystals: 1

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Sample preparation

CrystalDensity Matthews: 3.35 Å3/Da / Density % sol: 63.33 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / pH: 8.5
Details: 1.26M ammonium sulfate, 0.1M Tris, 0.2M lithium sulfate, pH 8.5, VAPOR DIFFUSION, HANGING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL7-1 / Wavelength: 0.97773 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Jan 1, 2007 / Details: mirrors
RadiationMonochromator: side scattering I-beam bent single crystal, asymmetric cut 4.9650 deg
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97773 Å / Relative weight: 1
ReflectionResolution: 2.42→101.53 Å / Num. obs: 57700 / % possible obs: 100 % / Redundancy: 14.2 % / Rmerge(I) obs: 0.09
Reflection shellResolution: 2.42→2.55 Å / Redundancy: 14.6 % / Rmerge(I) obs: 0.372 / Mean I/σ(I) obs: 23.8 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 3BPM

3bpm


Resolution: 2.42→101.53 Å / Cor.coef. Fo:Fc: 0.945 / Cor.coef. Fo:Fc free: 0.934 / SU B: 9.405 / SU ML: 0.126 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.263 / ESU R Free: 0.199 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20886 2924 5.1 %RANDOM
Rwork0.17459 ---
obs0.17637 54685 99.95 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 25.83 Å2
Baniso -1Baniso -2Baniso -3
1-0.97 Å20 Å20 Å2
2--0.97 Å20 Å2
3----1.94 Å2
Refinement stepCycle: LAST / Resolution: 2.42→101.53 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7505 0 173 497 8175
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.0227900
X-RAY DIFFRACTIONr_bond_other_d0.0020.025359
X-RAY DIFFRACTIONr_angle_refined_deg1.491.97510698
X-RAY DIFFRACTIONr_angle_other_deg0.9463.00912786
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.6245947
X-RAY DIFFRACTIONr_dihedral_angle_2_deg34.42224.492374
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.709151245
X-RAY DIFFRACTIONr_dihedral_angle_4_deg13.3691530
X-RAY DIFFRACTIONr_chiral_restr0.0930.21082
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.028841
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021661
X-RAY DIFFRACTIONr_nbd_refined0.1850.21338
X-RAY DIFFRACTIONr_nbd_other0.1910.25391
X-RAY DIFFRACTIONr_nbtor_refined0.1860.23801
X-RAY DIFFRACTIONr_nbtor_other0.0890.23941
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1560.2464
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.010.21
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2990.211
X-RAY DIFFRACTIONr_symmetry_vdw_other0.160.224
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1670.216
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.81.56031
X-RAY DIFFRACTIONr_mcbond_other0.151.51960
X-RAY DIFFRACTIONr_mcangle_it1.05427485
X-RAY DIFFRACTIONr_scbond_it1.87334040
X-RAY DIFFRACTIONr_scangle_it2.6794.53211
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.42→2.483 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.242 220 -
Rwork0.189 3998 -
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)
11.8746-0.4154-0.21351.81330.19921.4218-0.06430.06520.1104-0.06850.0714-0.059-0.154-0.0612-0.0071-0.11280.0178-0.0405-0.0633-0.0222-0.13733.9835-10.880342.1431
21.81350.3593-0.1151.74250.40681.4273-0.0881-0.0847-0.1275-0.05520.00490.04490.0801-0.09830.0833-0.1302-0.03730.0495-0.0095-0.0861-0.11143.7747-47.085417.0946
31.51470.0729-0.28721.9601-0.39042.1186-0.21930.0678-0.259-0.05540.10710.00920.2023-0.17780.1122-0.1062-0.0160.1196-0.0842-0.0275-0.1007-3.5541-49.060244.2839
41.634-0.11-0.09422.44150.52761.9007-0.02190.14860.0475-0.4737-0.05680.1425-0.3198-0.34650.07870.02610.079-0.1198-0.003-0.0256-0.185-8.1843-9.823216.8523
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A0 - 241
2X-RAY DIFFRACTION2B0 - 241
3X-RAY DIFFRACTION3C-1 - 241
4X-RAY DIFFRACTION4D0 - 241

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