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- PDB-3bpf: Crystal Structure of Falcipain-2 with Its inhibitor, E64 -

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Basic information

Entry
Database: PDB / ID: 3bpf
TitleCrystal Structure of Falcipain-2 with Its inhibitor, E64
ComponentsCysteine protease falcipain-2
KeywordsHYDROLASE / falcipain / malaria / cysteine protease / Thiol protease
Function / homology
Function and homology information


cysteine-type peptidase activity / proteolysis involved in protein catabolic process / membrane => GO:0016020 / Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases / lysosome / cysteine-type endopeptidase activity / extracellular space / membrane
Similarity search - Function
Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / Peptidase C1A, papain C-terminal / Papain family cysteine protease / Papain family cysteine protease ...Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Cathepsin propeptide inhibitor domain (I29) / Papain-like cysteine endopeptidase / : / Cysteine peptidase, histidine active site / Eukaryotic thiol (cysteine) proteases histidine active site. / 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-E64 / Falcipain 2 / Cysteine protease falcipain-2
Similarity search - Component
Biological speciesPlasmodium falciparum (malaria parasite P. falciparum)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.9 Å
Authorskerr, I.D. / Lee, J.H. / Brinen, L.S.
CitationJournal: J.Med.Chem. / Year: 2009
Title: Structures of falcipain-2 and falcipain-3 bound to small molecule inhibitors: implications for substrate specificity.
Authors: Kerr, I.D. / Lee, J.H. / Pandey, K.C. / Harrison, A. / Sajid, M. / Rosenthal, P.J. / Brinen, L.S.
History
DepositionDec 18, 2007Deposition site: RCSB / Processing site: RCSB
Revision 1.0Dec 30, 2008Provider: repository / Type: Initial release
Revision 1.1Jul 13, 2011Group: Advisory / Refinement description / Version format compliance
Revision 1.2Aug 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

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Cysteine protease falcipain-2
B: Cysteine protease falcipain-2
C: Cysteine protease falcipain-2
D: Cysteine protease falcipain-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)110,2809
Polymers108,7474
Non-polymers1,5345
Water75742
1
A: Cysteine protease falcipain-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5472
Polymers27,1871
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
2
B: Cysteine protease falcipain-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5472
Polymers27,1871
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
C: Cysteine protease falcipain-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,6393
Polymers27,1871
Non-polymers4532
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
4
D: Cysteine protease falcipain-2
hetero molecules


Theoretical massNumber of molelcules
Total (without water)27,5472
Polymers27,1871
Non-polymers3601
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)143.778, 167.810, 177.758
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number20
Space group name H-MC2221

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Components

#1: Protein
Cysteine protease falcipain-2


Mass: 27186.672 Da / Num. of mol.: 4 / Source method: isolated from a natural source
Source: (natural) Plasmodium falciparum (malaria parasite P. falciparum)
References: UniProt: Q9NBD4, UniProt: Q9N6S8*PLUS, Hydrolases; Acting on peptide bonds (peptidases); Cysteine endopeptidases
#2: Chemical
ChemComp-E64 / N-[N-[1-HYDROXYCARBOXYETHYL-CARBONYL]LEUCYLAMINO-BUTYL]-GUANIDINE


Mass: 360.429 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C15H30N5O5
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 42 / Source method: isolated from a natural source / Formula: H2O
Sequence detailsAUTHORS STATE THAT THIS RESIDUE IS CONSERVATIVELY SUBSTITUTED AMONGST DIFFERENT STRAINS, BUT SHOULD ...AUTHORS STATE THAT THIS RESIDUE IS CONSERVATIVELY SUBSTITUTED AMONGST DIFFERENT STRAINS, BUT SHOULD BE GLN IN THIS STRUCTURE.

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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: 4.93 Å3/Da / Density % sol: 75.05 %
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 6
Details: 100 mM Sodium Citrate, 10% PEG 3350, 100 mM Magnesium Formate, 5% Glycerol, pH 6.0, VAPOR DIFFUSION, SITTING DROP, temperature 298K

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Data collection

DiffractionMean temperature: 93 K
Diffraction sourceSource: SYNCHROTRON / Site: SSRL / Beamline: BL9-1 / Wavelength: 0.979 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Mar 8, 2006 / Details: mirrors
RadiationMonochromator: Side-scattering cuberoot I-beam bent single crystal
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.979 Å / Relative weight: 1
ReflectionResolution: 2.83→66.7 Å / Num. obs: 45440 / % possible obs: 99.3 % / Observed criterion σ(I): 3 / Redundancy: 7.3 % / Rsym value: 0.201 / Net I/σ(I): 10.04
Reflection shellResolution: 2.83→2.99 Å / Redundancy: 7.04 % / Rmerge(I) obs: 0.653 / Mean I/σ(I) obs: 1.22 / % possible all: 96.5

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
ADSCQuantumdata collection
MOSFLMdata reduction
XSCALEdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1YVB

1yvb


Resolution: 2.9→66.67 Å / Cor.coef. Fo:Fc: 0.894 / Cor.coef. Fo:Fc free: 0.834 / SU B: 38.493 / SU ML: 0.424 / TLS residual ADP flag: LIKELY RESIDUAL / Cross valid method: THROUGHOUT / ESU R: 0.561 / ESU R Free: 0.389 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.32542 2418 5.1 %RANDOM
Rwork0.27546 ---
obs0.27794 45440 99.9 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 66.289 Å2
Baniso -1Baniso -2Baniso -3
1-0.58 Å20 Å20 Å2
2---1.22 Å20 Å2
3---0.65 Å2
Refinement stepCycle: LAST / Resolution: 2.9→66.67 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7305 0 106 42 7453
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0227586
X-RAY DIFFRACTIONr_bond_other_d0.0010.025168
X-RAY DIFFRACTIONr_angle_refined_deg1.0491.96110196
X-RAY DIFFRACTIONr_angle_other_deg0.8123.00412493
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.4585917
X-RAY DIFFRACTIONr_dihedral_angle_2_deg35.3425.245368
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.389151283
X-RAY DIFFRACTIONr_dihedral_angle_4_deg10.9281526
X-RAY DIFFRACTIONr_chiral_restr0.0620.21055
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.028489
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021541
X-RAY DIFFRACTIONr_nbd_refined0.2050.22041
X-RAY DIFFRACTIONr_nbd_other0.1770.25797
X-RAY DIFFRACTIONr_nbtor_refined0.1840.23729
X-RAY DIFFRACTIONr_nbtor_other0.0840.23896
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1670.2271
X-RAY DIFFRACTIONr_xyhbond_nbd_other0.0860.22
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.1450.219
X-RAY DIFFRACTIONr_symmetry_vdw_other0.1740.239
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1340.21
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.3581.55905
X-RAY DIFFRACTIONr_mcbond_other0.0351.51908
X-RAY DIFFRACTIONr_mcangle_it0.41927296
X-RAY DIFFRACTIONr_scbond_it0.5433689
X-RAY DIFFRACTIONr_scangle_it0.7094.52900
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.9→2.975 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.435 161 -
Rwork0.407 3332 -
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)
111.45660.21023.21892.30321.26456.2113-0.1878-1.44940.17160.0841-0.1591-0.06490.1584-0.03740.3469-0.08990.1859-0.014-0.7264-0.0545-0.4126-47.6073-12.3998-12.9289
21.20330.29850.21734.5429-0.96833.67770.09820.46590.57250.0230.0329-0.28370.28250.1099-0.1311-0.2432-0.4361-0.268-0.15010.50440.1635-46.928218.207-43.1225
31.9692-0.97750.4224.2309-2.43216.2996-0.0169-0.373-0.11210.3222-0.26990.38670.1491-0.81410.2868-0.37950.1283-0.07590.2301-0.5013-0.0812-84.0694-6.893-20.9247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A1 - 241
2X-RAY DIFFRACTION2B1 - 240
3X-RAY DIFFRACTION3C2 - 241

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