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- PDB-9h8w: Leishmania donovani ISP2 in complex with bovine alpha-chymotrypsin -

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Basic information

Entry
Database: PDB / ID: 9h8w
TitleLeishmania donovani ISP2 in complex with bovine alpha-chymotrypsin
Components
  • Chymotrypsinogen A
  • Ecotin family protein
KeywordsHYDROLASE / ecotin-like inhibitor / complex / protease / Leishmania
Function / homology
Function and homology information


chymotrypsin / serpin family protein binding / serine protease inhibitor complex / digestion / serine-type endopeptidase inhibitor activity / serine-type endopeptidase activity / ATP hydrolysis activity / proteolysis / extracellular region / ATP binding
Similarity search - Function
Proteinase inhibitor I11, ecotin / Ecotin superfamily / Ecotin / : / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core ...Proteinase inhibitor I11, ecotin / Ecotin superfamily / Ecotin / : / AAA ATPase, AAA+ lid domain / AAA+ lid domain / ATPase, AAA-type, conserved site / AAA-protein family signature. / ATPase family associated with various cellular activities (AAA) / ATPase, AAA-type, core / Serine proteases, trypsin family, histidine active site / Serine proteases, trypsin family, serine active site / Serine proteases, trypsin family, histidine active site. / Peptidase S1A, chymotrypsin family / Serine proteases, trypsin family, serine active site. / Serine proteases, trypsin domain profile. / Trypsin-like serine protease / Serine proteases, trypsin domain / Trypsin / ATPases associated with a variety of cellular activities / AAA+ ATPase domain / Peptidase S1, PA clan, chymotrypsin-like fold / Peptidase S1, PA clan / P-loop containing nucleoside triphosphate hydrolase
Similarity search - Domain/homology
Ecotin-like protein 2 / Chymotrypsinogen A
Similarity search - Component
Biological speciesLeishmania donovani (eukaryote)
Bos taurus (domestic cattle)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2 Å
AuthorsFreitag-Pohl, S. / Pohl, E.
Funding support United Kingdom, 1items
OrganizationGrant numberCountry
UK Research and Innovation (UKRI)MR/P027989/1 United Kingdom
CitationJournal: To Be Published
Title: Deciphering the Interactions of Leishmanial Serine Protease Inhibitors ISP2 and Proteases
Authors: Freitag-Pohl, S. / Pohl, E.
History
DepositionOct 29, 2024Deposition site: PDBE / Processing site: PDBE
Revision 1.0May 13, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Ecotin family protein
C: Ecotin family protein
B: Chymotrypsinogen A
D: Chymotrypsinogen A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,1499
Polymers86,8894
Non-polymers2615
Water3,441191
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10050 Å2
ΔGint-75 kcal/mol
Surface area29040 Å2
MethodPISA
Unit cell
Length a, b, c (Å)88.013, 90.799, 96.645
Angle α, β, γ (deg.)90, 90, 90
Int Tables number19
Space group name H-MP212121
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails (eV)
11A
21A
32A
42A

NCS domain segments:
Dom-IDComponent-IDEns-IDBeg auth comp-IDBeg label comp-IDEnd auth comp-IDEnd label comp-IDAuth asym-IDLabel asym-IDAuth seq-IDLabel seq-ID
111ASNASNGLUGLUAA15 - 15715 - 157
211ASNASNGLUGLUAA15 - 15715 - 157
322CYSCYSASNASNBC1 - 2451 - 245
422CYSCYSASNASNBC1 - 2451 - 245

NCS ensembles :
IDDetails (eV)
1Local NCS retraints between domains: 1 2
2Local NCS retraints between domains: 3 4

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Components

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Protein , 2 types, 4 molecules ACBD

#1: Protein Ecotin family protein


Mass: 17758.393 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania donovani (eukaryote) / Gene: CGC20_30130 / Production host: Escherichia coli (E. coli) / References: UniProt: A0A504Y4D3
#2: Protein Chymotrypsinogen A


Mass: 25686.037 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Bos taurus (domestic cattle) / Production host: Escherichia coli (E. coli) / References: UniProt: P00766, chymotrypsin

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Non-polymers , 4 types, 196 molecules

#3: Chemical ChemComp-CL / CHLORIDE ION


Mass: 35.453 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Cl
#4: Chemical ChemComp-EDO / 1,2-ETHANEDIOL / ETHYLENE GLYCOL


Mass: 62.068 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C2H6O2
#5: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


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


Mass: 18.015 Da / Num. of mol.: 191 / Source method: isolated from a natural source / Formula: H2O

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Details

Has ligand of interestN
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: 2.22 Å3/Da / Density % sol: 44.65 % / Description: block
Crystal growTemperature: 298 K / Method: vapor diffusion, sitting drop / pH: 7 / Details: 0.15 M DL-Malic acid 20 % w/v PEG 3350

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: Diamond / Beamline: I04 / Wavelength: 0.97499 Å
DetectorType: DECTRIS EIGER2 XE 16M / Detector: PIXEL / Date: May 25, 2022
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.97499 Å / Relative weight: 1
ReflectionResolution: 2→48.37 Å / Num. obs: 53201 / % possible obs: 100 % / Redundancy: 54 % / CC1/2: 0.999 / Rmerge(I) obs: 0.199 / Rpim(I) all: 0.027 / Rrim(I) all: 0.201 / Net I/σ(I): 11.5
Reflection shellResolution: 2→2.03 Å / Redundancy: 51.5 % / Rmerge(I) obs: 2.082 / Mean I/σ(I) obs: 0.6 / Num. unique obs: 2604 / CC1/2: 0.875 / Rpim(I) all: 0.291 / Rrim(I) all: 2.103 / % possible all: 100

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Processing

Software
NameVersionClassification
REFMAC5.8.0425refinement
xia2.multiplexdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2→48.369 Å / Cor.coef. Fo:Fc: 0.954 / Cor.coef. Fo:Fc free: 0.924 / SU B: 7.003 / SU ML: 0.181 / Cross valid method: FREE R-VALUE / ESU R: 0.201 / ESU R Free: 0.188
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.2738 2682 5.05 %
Rwork0.2156 50432 -
all0.218 --
obs-53114 99.889 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL PLUS MASK
Displacement parametersBiso mean: 48.305 Å2
Baniso -1Baniso -2Baniso -3
1-4.69 Å2-0 Å20 Å2
2---0.376 Å2-0 Å2
3----4.313 Å2
Refinement stepCycle: LAST / Resolution: 2→48.369 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5557 0 13 191 5761
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0125701
X-RAY DIFFRACTIONr_bond_other_d0.0010.0165168
X-RAY DIFFRACTIONr_angle_refined_deg1.5491.7877799
X-RAY DIFFRACTIONr_angle_other_deg0.5181.72111916
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.6265747
X-RAY DIFFRACTIONr_dihedral_angle_2_deg9.888522
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.76410825
X-RAY DIFFRACTIONr_dihedral_angle_6_deg14.54310202
X-RAY DIFFRACTIONr_chiral_restr0.0680.2915
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.026760
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021268
X-RAY DIFFRACTIONr_nbd_refined0.1990.2993
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2020.24778
X-RAY DIFFRACTIONr_nbtor_refined0.1790.22854
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.090.22976
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.1570.2241
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0150.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.2660.211
X-RAY DIFFRACTIONr_nbd_other0.1910.233
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1240.23
X-RAY DIFFRACTIONr_mcbond_it4.7874.8543012
X-RAY DIFFRACTIONr_mcbond_other4.7874.8543012
X-RAY DIFFRACTIONr_mcangle_it6.238.6973745
X-RAY DIFFRACTIONr_mcangle_other6.238.6973746
X-RAY DIFFRACTIONr_scbond_it4.9415.0092689
X-RAY DIFFRACTIONr_scbond_other4.9415.0092690
X-RAY DIFFRACTIONr_scangle_it6.7449.1544052
X-RAY DIFFRACTIONr_scangle_other6.7449.1534053
X-RAY DIFFRACTIONr_lrange_it8.24647.2616144
X-RAY DIFFRACTIONr_lrange_other8.24647.2626145
X-RAY DIFFRACTIONr_ncsr_local_group_10.1110.053737
X-RAY DIFFRACTIONr_ncsr_local_group_20.0770.056899
Refine LS restraints NCS
Ens-IDDom-IDAuth asym-IDRefine-IDTypeRms dev position (Å)Weight position
11AX-RAY DIFFRACTIONLocal ncs0.110990.05008
12AX-RAY DIFFRACTIONLocal ncs0.110990.05008
23AX-RAY DIFFRACTIONLocal ncs0.077120.05009
24AX-RAY DIFFRACTIONLocal ncs0.077120.05009
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2-2.050.371860.3473662X-RAY DIFFRACTION99.1242
2.05-2.1060.3321940.3173601X-RAY DIFFRACTION100
2.106-2.1670.3292040.2963451X-RAY DIFFRACTION100
2.167-2.2330.3151720.2653380X-RAY DIFFRACTION100
2.233-2.3060.2982080.2473297X-RAY DIFFRACTION100
2.306-2.3870.2911710.2343179X-RAY DIFFRACTION100
2.387-2.4770.3431680.2633070X-RAY DIFFRACTION99.9691
2.477-2.5780.3411810.2442935X-RAY DIFFRACTION100
2.578-2.6920.3331540.2172851X-RAY DIFFRACTION100
2.692-2.8230.3111710.2232716X-RAY DIFFRACTION100
2.823-2.9750.2881190.2152614X-RAY DIFFRACTION100
2.975-3.1550.2651230.2112481X-RAY DIFFRACTION100
3.155-3.3720.2291240.1882324X-RAY DIFFRACTION100
3.372-3.640.2221200.1892172X-RAY DIFFRACTION100
3.64-3.9860.271080.2022016X-RAY DIFFRACTION100
3.986-4.4520.249930.1861822X-RAY DIFFRACTION100
4.452-5.1340.248740.1781645X-RAY DIFFRACTION100
5.134-6.270.207410.2111434X-RAY DIFFRACTION100
6.27-8.7940.225390.2021126X-RAY DIFFRACTION100
8.794-48.3690.262320.222656X-RAY DIFFRACTION97.1751

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