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- PDB-6wl6: Cocomplex structure of Deoxyhypusine synthase with inhibitor 6-[(... -

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Basic information

Entry
Database: PDB / ID: 6wl6
TitleCocomplex structure of Deoxyhypusine synthase with inhibitor 6-[(2R)-1-AMINO-4-METHYLPENTAN-2-YL]-3-(PYRIDIN-3-YL)-4H,5H,6H,7H-THIENO[2,3-C]PYRIDIN-7-ONE
ComponentsDeoxyhypusine synthase
KeywordsTRANSFERASE/INHIBITOR / Deoxyhypusine / Inhibitor / Transferase / TRANSFERASE-INHIBITOR complex
Function / homology
Function and homology information


peptidyl-lysine modification to peptidyl-hypusine / 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-lysine modification to peptidyl-hypusine / 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 / cytoplasm / cytosol
Similarity search - Function
Deoxyhypusine Synthase / Deoxyhypusine synthase / Deoxyhypusine synthase / Deoxyhypusine synthase superfamily / Deoxyhypusine synthase / DHS-like NAD/FAD-binding domain superfamily / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-91A / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.12 Å
AuthorsKlein, M.G. / Ambrus-Aikelin, G.
CitationJournal: Acs Med.Chem.Lett. / Year: 2020
Title: New Series of Potent Allosteric Inhibitors of Deoxyhypusine Synthase.
Authors: Tanaka, Y. / Kurasawa, O. / Yokota, A. / Klein, M.G. / Saito, B. / Matsumoto, S. / Okaniwa, M. / Ambrus-Aikelin, G. / Uchiyama, N. / Morishita, D. / Kimura, H. / Imamura, S.
History
DepositionApr 18, 2020Deposition site: RCSB / Processing site: RCSB
Revision 1.0Aug 19, 2020Provider: repository / Type: Initial release
Revision 1.1Aug 25, 2021Group: Database references / Category: citation / database_2
Item: _citation.journal_volume / _citation.page_first ..._citation.journal_volume / _citation.page_first / _citation.page_last / _citation.pdbx_database_id_PubMed / _citation.title / _database_2.pdbx_DOI / _database_2.pdbx_database_accession
Revision 1.2Oct 18, 2023Group: Data collection / Refinement description
Category: chem_comp_atom / chem_comp_bond / pdbx_initial_refinement_model

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

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


Theoretical massNumber of molelcules
Total (without water)83,0864
Polymers82,4272
Non-polymers6592
Water3,459192
1
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules

A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,1728
Polymers164,8544
Non-polymers1,3184
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_675x-y+1,-y+2,-z+1/31
Buried area19940 Å2
ΔGint-130 kcal/mol
Surface area41820 Å2
MethodPISA
Unit cell
Length a, b, c (Å)105.988, 105.988, 157.068
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number154
Space group name H-MP3221

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Components

#1: Protein Deoxyhypusine synthase / DHS


Mass: 41213.613 Da / Num. of mol.: 2
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: Chemical ChemComp-91A / 6-[(2R)-1-amino-4-methylpentan-2-yl]-3-(pyridin-3-yl)-5,6-dihydrothieno[2,3-c]pyridin-7(4H)-one


Mass: 329.460 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C18H23N3OS / Feature type: SUBJECT OF INVESTIGATION
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 192 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 3.09 Å3/Da / Density % sol: 60.19 %
Crystal growTemperature: 298 K / Method: vapor diffusion, hanging drop / Details: 100mM Hepes, 2.0M Na/K Phosphate

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: NSLS / Beamline: X6A / Wavelength: 1.078 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Mar 7, 2013
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.078 Å / Relative weight: 1
ReflectionResolution: 2.12→50 Å / Num. obs: 58565 / % possible obs: 95.4 % / Redundancy: 3.7 % / Rsym value: 0.135 / Net I/σ(I): 15.55
Reflection shellResolution: 2.12→2.16 Å / Num. unique obs: 3184 / Rsym value: 0.94

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Processing

Software
NameVersionClassification
REFMAC5.7.0025refinement
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 6P4V

6p4v


Resolution: 2.12→43.97 Å / Cor.coef. Fo:Fc: 0.957 / Cor.coef. Fo:Fc free: 0.949 / SU B: 7.833 / SU ML: 0.089 / Cross valid method: THROUGHOUT / ESU R: 0.147 / ESU R Free: 0.128 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.1944 2845 5.1 %RANDOM
Rwork0.17872 ---
obs0.17953 53246 99.94 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 34.141 Å2
Baniso -1Baniso -2Baniso -3
1-1.3 Å20.65 Å20 Å2
2--1.3 Å20 Å2
3----1.94 Å2
Refinement stepCycle: 1 / Resolution: 2.12→43.97 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms4528 0 46 192 4766
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.024725
X-RAY DIFFRACTIONr_bond_other_d0.0010.024462
X-RAY DIFFRACTIONr_angle_refined_deg1.2121.9716420
X-RAY DIFFRACTIONr_angle_other_deg0.748310250
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.4995591
X-RAY DIFFRACTIONr_dihedral_angle_2_deg32.52524.811212
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.05315786
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.8831522
X-RAY DIFFRACTIONr_chiral_restr0.070.2726
X-RAY DIFFRACTIONr_gen_planes_refined0.0050.0215371
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021073
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_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.15→2.206 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.318 200 -
Rwork0.255 3903 -
obs--99.95 %
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)
10.205-0.03190.1760.653-0.292.231-0.06090.03830.04160.10660.0726-0.019-0.21750.1099-0.01170.0734-0.0171-0.0120.0282-0.00680.058311.4042114.033935.7354
20.2201-0.368-0.24411.50970.76231.113-0.0611-0.0245-0.01380.17280.0964-0.06540.02530.1513-0.03530.1110.0668-0.01480.08370.00680.067611.616889.017350.2169
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A28 - 363
2X-RAY DIFFRACTION1B701
3X-RAY DIFFRACTION1A801 - 885
4X-RAY DIFFRACTION1B858
5X-RAY DIFFRACTION2B28 - 362
6X-RAY DIFFRACTION2A701

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