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- PDB-6pgr: Cocomplex structure of Deoxyhypusine synthase with inhibitor 6-BR... -

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Basic information

Entry
Database: PDB / ID: 6pgr
TitleCocomplex structure of Deoxyhypusine synthase with inhibitor 6-BROMO-N-(1H-INDOL-4-YL)-1-BENZOTHIOPHENE-2-CARBOXAMIDE
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-8XY / Deoxyhypusine synthase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.95 Å
AuthorsKlein, M.G. / Ambrus-Aikelin, G.
CitationJournal: J.Med.Chem. / Year: 2020
Title: Discovery of Novel Allosteric Inhibitors of Deoxyhypusine Synthase.
Authors: Tanaka, Y. / Kurasawa, O. / Yokota, A. / Klein, M.G. / Ono, K. / Saito, B. / Matsumoto, S. / Okaniwa, M. / Ambrus-Aikelin, G. / Morishita, D. / Kitazawa, S. / Uchiyama, N. / Ogawa, K. / Kimura, H. / Imamura, S.
History
DepositionJun 24, 2019Deposition site: RCSB / Processing site: RCSB
Revision 1.0Apr 1, 2020Provider: repository / Type: Initial release
Revision 1.1Apr 8, 2020Group: Database references / Category: citation
Item: _citation.journal_volume / _citation.page_first / _citation.page_last
Revision 1.2Oct 11, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession

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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)83,1704
Polymers82,4272
Non-polymers7432
Water6,449358
1
A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules

A: Deoxyhypusine synthase
B: Deoxyhypusine synthase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)166,3398
Polymers164,8544
Non-polymers1,4854
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation5_555x-y,-y,-z+1/31
Buried area27270 Å2
ΔGint-164 kcal/mol
Surface area44360 Å2
MethodPISA
Unit cell
Length a, b, c (Å)104.584, 104.584, 160.489
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-8XY / 6-bromo-N-(1H-indol-4-yl)-1-benzothiophene-2-carboxamide


Mass: 371.251 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C17H11BrN2OS
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 358 / Source method: isolated from a natural source / Formula: H2O

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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: 3.07 Å3/Da / Density % sol: 59.99 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop
Details: 1.6M SODIUM/POTASSIUM PHOSPHATE (PH 6.8), VAPOR DIFFUSION, HANGING DROP, TEMPERATURE 298K

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Data collection

DiffractionMean temperature: 95 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ALS / Beamline: 5.0.2 / Wavelength: 0.98 Å
DetectorType: ADSC QUANTUM 315 / Detector: CCD / Date: Oct 26, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.98 Å / Relative weight: 1
ReflectionResolution: 1.95→50 Å / Num. obs: 74394 / % possible obs: 100 % / Redundancy: 7.3 % / Net I/σ(I): 20.3
Reflection shellResolution: 1.95→1.98 Å / Num. unique obs: 3695

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Processing

Software
NameVersionClassification
HKL-2000data reduction
HKL-2000data scaling
PHASERphasing
REFMAC5.7.0025refinement
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 1RLZ.PDB

1rlz


Resolution: 1.95→49.77 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU B: 5.797 / SU ML: 0.074 / Cross valid method: THROUGHOUT / ESU R: 0.117 / ESU R Free: 0.111 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.194 3744 5 %RANDOM
Rwork0.168 ---
obs0.17 70577 100 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 31.27 Å2
Baniso -1Baniso -2Baniso -3
1-1.18 Å20.59 Å20 Å2
2--1.18 Å20 Å2
3----1.76 Å2
Refinement stepCycle: LAST / Resolution: 1.95→49.77 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5366 0 44 358 5768
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.0195587
X-RAY DIFFRACTIONr_bond_other_d0.0010.025305
X-RAY DIFFRACTIONr_angle_refined_deg1.2751.9667597
X-RAY DIFFRACTIONr_angle_other_deg0.773312174
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.3785709
X-RAY DIFFRACTIONr_dihedral_angle_2_deg37.84924.449254
X-RAY DIFFRACTIONr_dihedral_angle_3_deg13.27815940
X-RAY DIFFRACTIONr_dihedral_angle_4_deg17.511534
X-RAY DIFFRACTIONr_chiral_restr0.0770.2852
X-RAY DIFFRACTIONr_gen_planes_refined0.0060.0216440
X-RAY DIFFRACTIONr_gen_planes_other0.0010.021290
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: 1.95→2 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.261 262 -
Rwork0.22 5133 -
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)
10.00330.0080.02310.3387-0.15120.485-0.01410.0021-0.00080.03450.05290.0091-0.1131-0.0101-0.03880.06170.00550.00250.0213-0.00640.0472-42.654220.520535.6731
20.02860.00160.05160.60620.05370.3578-0.02550.0060.00430.11680.0689-0.04450.04270.0572-0.04340.0750.0432-0.01580.04980.00160.0191-37.8213-2.112348.9247
Refinement TLS group
IDRefine-IDRefine TLS-IDAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1A13 - 363
2X-RAY DIFFRACTION1A401
3X-RAY DIFFRACTION1A501 - 678
4X-RAY DIFFRACTION1B553 - 658
5X-RAY DIFFRACTION2B15 - 362
6X-RAY DIFFRACTION2B401

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