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- PDB-9idv: Human Deoxyhypusine Synthase Fragment Screening Campaign - ligand... -

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Basic information

Entry
Database: PDB / ID: 9idv
TitleHuman Deoxyhypusine Synthase Fragment Screening Campaign - ligand VT00216
Components(Deoxyhypusine ...) x 2
KeywordsTRANSFERASE / fragment screening / polyamines / high-throughput / posttranslational modifications
Function / homology
Function and homology information


peptidyl-hypusine biosynthetic process / deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation ...peptidyl-hypusine biosynthetic process / deoxyhypusine synthase / Hypusine synthesis from eIF5A-lysine / deoxyhypusine synthase activity / spermidine metabolic process / spermidine catabolic process / positive regulation of T cell proliferation / glucose homeostasis / translation / positive regulation of cell population proliferation / identical protein binding / cytosol / cytoplasm
Similarity search - Function
Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / DHS-like NAD/FAD-binding domain superfamily
Similarity search - Domain/homology
: / NICOTINAMIDE-ADENINE-DINUCLEOTIDE / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.33 Å
AuthorsWilk, P. / Wator-Wilk, E. / Krojer, T. / Grudnik, P.
Funding support Poland, 2items
OrganizationGrant numberCountry
Polish National Science CentreUMO-2019/33/B/NZ1/01839 Poland
Polish National Science CentreUMO-2022/47/B/NZ7/01667 Poland
CitationJournal: To Be Published
Title: Crystallographic fragment screening supports tool compound discovery and reveals conformational flexibility in human deoxyhypusine synthase
Authors: Wilk, P. / Wator-Wilk, E. / Muszak, D. / Kochanowski, P. / Krojer, T. / Grudnik, P.
History
DepositionFeb 15, 2025Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jan 21, 2026Provider: repository / Type: Initial release

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

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Assembly

Deposited unit
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)83,6906
Polymers82,1212
Non-polymers1,5694
Water8,899494
1
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules

A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)167,38012
Polymers164,2424
Non-polymers3,1388
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation4_555y,x,-z1
Buried area31050 Å2
ΔGint-184 kcal/mol
Surface area41980 Å2
Unit cell
Length a, b, c (Å)105.130, 105.130, 160.300
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221
Components on special symmetry positions
IDModelComponents
11A-724-

HOH

21B-658-

HOH

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Components

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Deoxyhypusine ... , 2 types, 2 molecules AB

#1: Protein Deoxyhypusine synthase / DHS


Mass: 41044.500 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHPS, DS / Production host: Escherichia coli (E. coli) / References: UniProt: P49366, deoxyhypusine synthase
#2: Protein Deoxyhypusine synthase / DHS


Mass: 41076.566 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: DHPS, DS / Production host: Escherichia coli (E. coli) / References: UniProt: P49366, deoxyhypusine synthase

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Non-polymers , 4 types, 498 molecules

#3: Chemical ChemComp-NAD / NICOTINAMIDE-ADENINE-DINUCLEOTIDE


Mass: 663.425 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C21H27N7O14P2 / Comment: NAD*YM
#4: Chemical ChemComp-MRD / (4R)-2-METHYLPENTANE-2,4-DIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#5: Chemical ChemComp-A1IGM / 1-methylpyrrole-2-carboxamide


Mass: 124.141 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H8N2O / Feature type: SUBJECT OF INVESTIGATION
#6: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 494 / Source method: isolated from a natural source / Formula: H2O

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Details

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: 3.11 Å3/Da / Density % sol: 60.5 %
Crystal growTemperature: 293 K / Method: vapor diffusion, sitting drop / pH: 8.5
Details: 0.025-0.125 mM carboxylic acid mix, 30-60% precipitant mix (MPD, PEG 1000, PEG 3350), 100 mM Tris-Bicine pH = 8.5'

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: MAX IV / Beamline: BioMAX / Wavelength: 0.9763 Å
DetectorType: DECTRIS EIGER2 X 16M / Detector: PIXEL / Date: Nov 13, 2021
RadiationMonochromator: Si(111), double crystal monochromator, horizontally deflecting,LN2 side-cooling
Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9763 Å / Relative weight: 1
ReflectionResolution: 1.33→46.08 Å / Num. obs: 219793 / % possible obs: 93.9 % / Redundancy: 10.08 % / CC1/2: 0.999 / Rmerge(I) obs: 0.059 / Rrim(I) all: 0.062 / Net I/av σ(I): 14.32 / Net I/σ(I): 14.32
Reflection shell

Diffraction-ID: 1

Resolution (Å)Rmerge(I) obsMean I/σ(I) obsNum. unique obsCC1/2Rrim(I) all% possible all
1.33-1.412.5790.4268540.4092.83371.5
1.41-1.511.585318380.7041.698
1.51-1.630.908328300.9070.953
1.63-1.780.461303750.9760.482
1.78-1.990.213274670.9930.222
1.99-2.30.104243570.9980.109
2.3-2.820.061207020.9990.064
2.82-3.980.037161480.9990.039
3.98-46.080.03692220.9990.037

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
XDSdata scaling
DIMPLEphasing
XDSdata reduction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.33→46.08 Å / Cor.coef. Fo:Fc: 0.977 / Cor.coef. Fo:Fc free: 0.973 / Cross valid method: THROUGHOUT / ESU R: 0.047 / ESU R Free: 0.048 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.20502 10928 5 %RANDOM
Rwork0.18957 ---
obs0.19038 208749 93.83 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK
Displacement parametersBiso mean: 29.04 Å2
Baniso -1Baniso -2Baniso -3
1--0 Å2-0 Å20 Å2
2---0 Å2-0 Å2
3---0.01 Å2
Refinement stepCycle: 1 / Resolution: 1.33→46.08 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5359 0 105 494 5958
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0180.0125699
X-RAY DIFFRACTIONr_bond_other_d0.0020.0165391
X-RAY DIFFRACTIONr_angle_refined_deg1.9261.6567768
X-RAY DIFFRACTIONr_angle_other_deg1.0271.57412401
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.9245715
X-RAY DIFFRACTIONr_dihedral_angle_2_deg6.561534
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.0710949
X-RAY DIFFRACTIONr_dihedral_angle_4_deg
X-RAY DIFFRACTIONr_chiral_restr0.0940.2875
X-RAY DIFFRACTIONr_gen_planes_refined0.0150.026735
X-RAY DIFFRACTIONr_gen_planes_other0.0150.021327
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_it2.5132.9672785
X-RAY DIFFRACTIONr_mcbond_other2.5052.9672785
X-RAY DIFFRACTIONr_mcangle_it3.3245.3423486
X-RAY DIFFRACTIONr_mcangle_other3.3235.3433487
X-RAY DIFFRACTIONr_scbond_it3.8153.2312914
X-RAY DIFFRACTIONr_scbond_other3.8143.232915
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other5.4545.824270
X-RAY DIFFRACTIONr_long_range_B_refined6.47731.286629
X-RAY DIFFRACTIONr_long_range_B_other6.47731.286630
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 1.33→1.365 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.505 585 -
Rwork0.51 10650 -
obs--65.55 %

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