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Basic information

Entry
Database: PDB / ID: 5go1
TitleStructural, Functional characterization and discovery of novel inhibitors of Leishmania amazonensis Nucleoside Diphosphatase Kinase (NDK)
ComponentsNucleoside diphosphate kinase
KeywordsTRANSFERASE / Kinase / Leishmania amazonensis / inhibitor
Function / homology
Function and homology information


nucleoside-diphosphate kinase / CTP biosynthetic process / UTP biosynthetic process / GTP biosynthetic process / nucleoside diphosphate kinase activity / ATP binding
Similarity search - Function
Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Nucleoside diphosphate kinase
Similarity search - Component
Biological speciesLeishmania amazonensis (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.5 Å
AuthorsMishra, A.K. / Agnihotri, P. / Singh, S.P. / Pratap, J.V.
CitationJournal: J. Comput. Aided Mol. Des. / Year: 2017
Title: Discovery of novel inhibitors for Leishmania nucleoside diphosphatase kinase (NDK) based on its structural and functional characterization.
Authors: Mishra, A.K. / Singh, N. / Agnihotri, P. / Mishra, S. / Singh, S.P. / Kolli, B.K. / Chang, K.P. / Sahasrabuddhe, A.A. / Siddiqi, M.I. / Pratap, J.V.
History
DepositionJul 26, 2016Deposition site: PDBJ / Processing site: PDBJ
Revision 1.0Jul 26, 2017Provider: repository / Type: Initial release
Revision 1.1Nov 8, 2023Group: Data collection / Database references / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / citation / database_2 / pdbx_initial_refinement_model
Item: _citation.country / _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: Nucleoside diphosphate kinase


Theoretical massNumber of molelcules
Total (without water)16,7141
Polymers16,7141
Non-polymers00
Water30617
1
A: Nucleoside diphosphate kinase
x 6


Theoretical massNumber of molelcules
Total (without water)100,2846
Polymers100,2846
Non-polymers00
Water1086
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
crystal symmetry operation2_565-y,x-y+1,z1
crystal symmetry operation3_455-x+y-1,-x,z1
crystal symmetry operation10_555-y,-x,-z+1/21
crystal symmetry operation11_455-x+y-1,y,-z+1/21
crystal symmetry operation12_565x,x-y+1,-z+1/21
Buried area9340 Å2
ΔGint-62 kcal/mol
Surface area25840 Å2
MethodPISA
Unit cell
Length a, b, c (Å)115.180, 115.180, 62.180
Angle α, β, γ (deg.)90.00, 90.00, 120.00
Int Tables number182
Space group name H-MP6322

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Components

#1: Protein Nucleoside diphosphate kinase


Mass: 16714.082 Da / Num. of mol.: 1
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Leishmania amazonensis (eukaryote) / Production host: Escherichia coli (E. coli) / Strain (production host): BL21(DE3)pLysS
References: UniProt: A0A1Y0DDB3*PLUS, nucleoside-diphosphate kinase
#2: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 17 / 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: 3.31 Å3/Da / Density % sol: 62.83 % / Description: hexagonal, compact, stable
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / pH: 6
Details: PEG MME 500, Bis-Tris Propane, Magnesium chloride, 30% ethylene glycol used as cryoprotectant
PH range: 5.8-7.0

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: BM14 / Wavelength: 0.954 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Nov 17, 2012 / Details: bent collimating mirror and toroid
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.954 Å / Relative weight: 1
ReflectionResolution: 2.5→99.75 Å / Num. obs: 8621 / % possible obs: 98.4 % / Redundancy: 13.8 % / Biso Wilson estimate: 65.4 Å2 / CC1/2: 0.99 / Rmerge(I) obs: 0.072 / Rsym value: 0.075 / Net I/σ(I): 19.8
Reflection shellResolution: 2.5→2.64 Å / Redundancy: 10.1 % / Rmerge(I) obs: 0.79 / Mean I/σ(I) obs: 2.3 / CC1/2: 0.768 / % possible all: 95.2

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Processing

Software
NameVersionClassification
REFMAC5.8.0135refinement
iMOSFLM7.0.9data reduction
SCALA3.3.16data scaling
PHASER2.3.0phasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 3NGR

3ngr


Resolution: 2.5→99.75 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.914 / SU B: 8.803 / SU ML: 0.187 / Cross valid method: THROUGHOUT / ESU R: 0.24 / ESU R Free: 0.218 / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2655 407 4.7 %RANDOM
Rwork0.22525 ---
obs0.22707 8201 97.29 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å
Displacement parametersBiso mean: 72.575 Å2
Baniso -1Baniso -2Baniso -3
1-1.44 Å20.72 Å2-0 Å2
2--1.44 Å2-0 Å2
3----4.67 Å2
Refinement stepCycle: LAST / Resolution: 2.5→99.75 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms814 0 0 17 831
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.020.019838
X-RAY DIFFRACTIONr_bond_other_d0.0030.02802
X-RAY DIFFRACTIONr_angle_refined_deg1.9921.9451135
X-RAY DIFFRACTIONr_angle_other_deg1.17231834
X-RAY DIFFRACTIONr_dihedral_angle_1_deg7.4235112
X-RAY DIFFRACTIONr_dihedral_angle_2_deg30.97322.35334
X-RAY DIFFRACTIONr_dihedral_angle_3_deg20.16715126
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.905158
X-RAY DIFFRACTIONr_chiral_restr0.1240.2126
X-RAY DIFFRACTIONr_gen_planes_refined0.010.021969
X-RAY DIFFRACTIONr_gen_planes_other0.0020.02195
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_it8.4237.222448
X-RAY DIFFRACTIONr_mcbond_other8.4117.21447
X-RAY DIFFRACTIONr_mcangle_it12.1710.781557
X-RAY DIFFRACTIONr_mcangle_other12.15910.798558
X-RAY DIFFRACTIONr_scbond_it7.0627.355390
X-RAY DIFFRACTIONr_scbond_other7.0627.355390
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other10.76210.947578
X-RAY DIFFRACTIONr_long_range_B_refined16.55467.3283647
X-RAY DIFFRACTIONr_long_range_B_other16.56167.343640
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.471 29 -
Rwork0.384 558 -
obs--92.15 %

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