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- PDB-9e6u: Crystal structure of human Taspase1 in complex with ligand SMDC1041556 -

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Basic information

Entry
Database: PDB / ID: 9e6u
TitleCrystal structure of human Taspase1 in complex with ligand SMDC1041556
ComponentsThreonine aspartase 1
KeywordsHYDROLASE/INHIBITOR / HYDROLASE-INHIBITOR complex
Function / homology
Function and homology information


Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases / Formation of WDR5-containing histone-modifying complexes / threonine-type endopeptidase activity / protein maturation / positive regulation of DNA-templated transcription / proteolysis / identical protein binding / cytoplasm / cytosol
Similarity search - Function
Threonine aspartase 1 / Peptidase T2, asparaginase 2 / Asparaginase / Nucleophile aminohydrolases, N-terminal
Similarity search - Domain/homology
: / Threonine aspartase 1
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.488 Å
AuthorsDoamekpor, S.K. / Hamilton, K. / Choi, P.H. / Tong, L.
Funding support United States, 1items
OrganizationGrant numberCountry
National Institutes of Health/National Cancer Institute (NIH/NCI) United States
CitationJournal: To Be Published
Title: Design and mechanism of potent inhibitors for the Mixed Lineage Leukemia (MLL) activating protease, Taspase-1
Authors: Doamekpor, S.K. / Hamilton, K. / Choi, P.H. / Tong, L. / Delker, S. / Waterson, A. / Neitz, J. / Sambucetti, L. / Arkin, M.
History
DepositionOct 31, 2024Deposition site: RCSB / Processing site: RCSB
Revision 1.0Nov 5, 2025Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Threonine aspartase 1
B: Threonine aspartase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)84,6556
Polymers83,6512
Non-polymers1,0054
Water00
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area2740 Å2
ΔGint-14 kcal/mol
Surface area22090 Å2
MethodPISA
Unit cell
Length a, b, c (Å)60.705, 93.902, 105.218
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number19
Space group name H-MP212121

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Components

#1: Protein Threonine aspartase 1 / Taspase-1


Mass: 41825.266 Da / Num. of mol.: 2
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: TASP1, C20orf13 / Production host: Escherichia coli (E. coli)
References: UniProt: Q9H6P5, Hydrolases; Acting on peptide bonds (peptidases); Threonine endopeptidases
#2: Chemical ChemComp-NA / SODIUM ION


Mass: 22.990 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: Na
#3: Chemical ChemComp-U47 / (2R)-4-(ethenylsulfonyl)-1-{[3-fluoro-4-(trifluoromethoxy)phenyl]methyl}-2-{[(1H-1,2,3-triazol-4-yl)methoxy]methyl}piperazine


Mass: 479.449 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H21F4N5O4S / Feature type: SUBJECT OF INVESTIGATION
Has ligand of interestY
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: 1.79 Å3/Da / Density % sol: 31.38 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 6.5 / Details: 20% MPD, 0.1 M MES, pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: APS / Beamline: 24-ID-C / Wavelength: 0.9791 Å
DetectorType: DECTRIS PILATUS3 S 6M / Detector: PIXEL / Date: Feb 17, 2018
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9791 Å / Relative weight: 1
ReflectionResolution: 2.488→70.059 Å / Num. obs: 21399 / % possible obs: 96.4 % / Redundancy: 2.708 % / Biso Wilson estimate: 59.71 Å2 / CC1/2: 0.998 / Rmerge(I) obs: 0.055 / Rrim(I) all: 0.068 / Χ2: 1.096 / Net I/σ(I): 11.16
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured obsNum. possibleNum. unique obsCC1/2Rrim(I) all% possible all
2.488-2.642.7090.671.4416687664161590.7360.82992.7
2.64-2.822.7910.372.6616948616660720.8790.45698.5
2.82-3.052.7410.1924.6615701578457280.9690.23799
3.05-3.342.5840.1027.8413438533352010.990.12797.5
3.34-3.732.7970.06413.9112886479146070.9950.07896.2
3.73-4.312.6970.04419.7910871422840310.9970.05495.3
4.31-5.272.5540.03324.568659357333900.9980.04194.9
5.27-7.452.7650.03126.417563278727350.9980.03898.1
7.45-70.0592.6690.027333860152414460.9980.03394.9

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Processing

Software
NameVersionClassification
XSCALEdata scaling
PHENIX1.12_2829refinement
PDB_EXTRACT3.25data extraction
XDSdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB entry 2A8J

2a8j


Resolution: 2.488→70.059 Å / SU ML: 0.4 / Cross valid method: THROUGHOUT / σ(F): 1.34 / Phase error: 34.63
RfactorNum. reflection% reflection
Rfree0.275 1997 9.35 %
Rwork0.1965 --
obs0.2037 21354 98.16 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å
Displacement parametersBiso max: 132.37 Å2 / Biso mean: 72.3998 Å2 / Biso min: 39.82 Å2
Refinement stepCycle: final / Resolution: 2.488→70.059 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4401 0 66 0 4467
Biso mean--73.6 --
Num. residues----607
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0154540
X-RAY DIFFRACTIONf_angle_d1.326143
X-RAY DIFFRACTIONf_chiral_restr0.058695
X-RAY DIFFRACTIONf_plane_restr0.007793
X-RAY DIFFRACTIONf_dihedral_angle_d18.6962667
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Rfactor Rfree error: 0

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection Rwork% reflection obs (%)
2.4884-2.55060.46241240.3493119686
2.5506-2.61960.39651430.32541378100
2.6196-2.69670.35841410.3071137599
2.6967-2.78370.37121410.27981371100
2.7837-2.88320.34641420.25441380100
2.8832-2.99860.35151450.24321393100
2.9986-3.13510.34891430.2191139099
3.1351-3.30040.29111410.2078135998
3.3004-3.50720.29571430.2114139199
3.5072-3.7780.27661450.175140699
3.778-4.15810.28051420.1642137398
4.1581-4.75970.1981450.1433141398
4.7597-5.99620.24551480.17861436100
5.9962-70.0590.23961540.1925149698

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