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- PDB-5dhp: Crystal structure of NAD kinase 1 from Listeria monocytogenes in ... -

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Basic information

Entry
Database: PDB / ID: 5dhp
TitleCrystal structure of NAD kinase 1 from Listeria monocytogenes in complex with a novel inhibitor
ComponentsNAD kinase 1NAD+ kinase
KeywordsTRANSFERASE / tetrameric NAD kinase
Function / homology
Function and homology information


NAD+ kinase / NADP biosynthetic process / NAD+ kinase activity / NAD metabolic process / NAD binding / phosphorylation / ATP binding / metal ion binding / cytoplasm
Similarity search - Function
Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / ATP-NAD kinase C-terminal domain / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tumour Suppressor Smad4 / Sandwich ...Probable inorganic polyphosphate/atp-NAD kinase; domain 1 / Probable inorganic polyphosphate/atp-NAD kinase; domain 2 / ATP-NAD kinase C-terminal domain / NAD kinase / ATP-NAD kinase, PpnK-type, C-terminal / ATP-NAD kinase N-terminal domain / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / NAD kinase/diacylglycerol kinase-like domain superfamily / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-5AQ / CITRIC ACID / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.27 Å
AuthorsGelin, M. / Paoletti, J. / Assairi, L. / Huteau, V. / Pochet, S. / Labesse, G.
Funding support France, 1items
OrganizationGrant numberCountry
French National Research AgencyANR-10-INSB-05-01 France
CitationJournal: Eur.J.Med.Chem. / Year: 2016
Title: 8-Thioalkyl-adenosine derivatives inhibit Listeria monocytogenes NAD kinase through a novel binding mode.
Authors: Paoletti, J. / Assairi, L. / Gelin, M. / Huteau, V. / Nahori, M.A. / Dussurget, O. / Labesse, G. / Pochet, S.
History
DepositionAug 31, 2015Deposition site: RCSB / Processing site: PDBE
Revision 1.0Sep 14, 2016Provider: repository / Type: Initial release
Revision 1.1Nov 9, 2016Group: Database references
Revision 1.2Sep 6, 2017Group: Author supporting evidence / Data collection / Category: diffrn_radiation_wavelength / pdbx_audit_support / Item: _pdbx_audit_support.funding_organization
Revision 1.3Jan 10, 2024Group: 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

Downloads & links

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Assembly

Deposited unit
A: NAD kinase 1
B: NAD kinase 1
C: NAD kinase 1
D: NAD kinase 1
hetero molecules


Theoretical massNumber of molelcules
Total (without water)126,69212
Polymers124,1814
Non-polymers2,5108
Water5,134285
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10720 Å2
ΔGint-44 kcal/mol
Surface area40460 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.930, 119.530, 67.310
Angle α, β, γ (deg.)90.00, 100.28, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NAD kinase 1 / NAD+ kinase / ATP-dependent NAD kinase


Mass: 31045.279 Da / Num. of mol.: 4
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Listeria monocytogenes serovar 1/2a (strain ATCC BAA-679 / EGD-e) (bacteria)
Gene: nadK1, lmo0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-CIT / CITRIC ACID / Citric acid


Mass: 192.124 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C6H8O7
#3: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL / Glycerol


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-5AQ / 8-({2-oxo-2-[(2-phenylethyl)amino]ethyl}sulfanyl)adenosine


Mass: 460.507 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H24N6O5S
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 285 / 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: 2.13 Å3/Da / Density % sol: 42.34 %
Crystal growTemperature: 291.15 K / Method: vapor diffusion, hanging drop / pH: 5
Details: 30 mM sodium bromide, 220 mM potassium citrate, pH 4.8-5.1, glycerol 6%, 15-16% w/v polyethylene glycol 400

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID14-1 / Wavelength: 0.9334 Å
DetectorType: ADSC QUANTUM 210 / Detector: CCD / Date: Sep 16, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.27→66.229 Å / Num. all: 46354 / Num. obs: 46354 / % possible obs: 96.4 % / Redundancy: 2.6 % / Biso Wilson estimate: 38.67 Å2 / Rpim(I) all: 0.027 / Rrim(I) all: 0.044 / Rsym value: 0.031 / Net I/av σ(I): 19.446 / Net I/σ(I): 15.7 / Num. measured all: 121261
Reflection shell

Diffraction-ID: 1 / Rejects: 0

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.27-2.392.60.3382.21813270290.3090.3382.199.9
2.39-2.542.60.2353.21734566040.2030.2353100
2.54-2.712.60.1551444154960.1310.154.688.6
2.71-2.932.60.0997.61534758090.0840.0996.9100
2.93-3.212.60.054141388653610.0460.05412100
3.21-3.592.60.02628.61145844360.0230.02621.591.9
3.59-4.152.60.01640.7936136310.0140.01632.385.3
4.15-5.082.70.01155.4974436190.0090.01143.7100
5.08-7.182.60.01345.9735928080.0110.01340.399.9
7.18-44.2572.70.01228.9418815610.010.01251.399.4

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Processing

Software
NameVersionClassification
PHENIX1.9_1692refinement
SCALA3.3.21data scaling
PDB_EXTRACT3.15data extraction
MOSFLMdata reduction
PHENIXphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: 2i1w

2i1w


Resolution: 2.27→44.257 Å / SU ML: 0.35 / Cross valid method: FREE R-VALUE / σ(F): 0.33 / Phase error: 31.65 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2585 2777 3.05 %
Rwork0.2174 --
obs0.2187 46196 96.09 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.27→44.257 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8145 0 173 285 8603
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0048546
X-RAY DIFFRACTIONf_angle_d0.63211574
X-RAY DIFFRACTIONf_dihedral_angle_d11.5373074
X-RAY DIFFRACTIONf_chiral_restr0.0261255
X-RAY DIFFRACTIONf_plane_restr0.0031477
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.2704-2.30950.45651440.39164511X-RAY DIFFRACTION98
2.3095-2.35150.41641170.37694558X-RAY DIFFRACTION99
2.3515-2.39670.36311520.35554617X-RAY DIFFRACTION99
2.3967-2.44560.35451670.34624493X-RAY DIFFRACTION99
2.4456-2.49880.35781450.32174624X-RAY DIFFRACTION100
2.4988-2.55690.30841310.31294511X-RAY DIFFRACTION100
2.5569-2.62090.34761260.29614656X-RAY DIFFRACTION100
2.6209-2.69170.3528830.28933334X-RAY DIFFRACTION71
2.6917-2.77090.37381230.28264586X-RAY DIFFRACTION100
2.7709-2.86030.28911430.26854575X-RAY DIFFRACTION100
2.8603-2.96260.34361410.26714579X-RAY DIFFRACTION100
2.9626-3.08110.29271520.25224602X-RAY DIFFRACTION100
3.0811-3.22130.29881540.22554612X-RAY DIFFRACTION100
3.2213-3.39110.24691720.20084547X-RAY DIFFRACTION100
3.3911-3.60350.2431310.18113823X-RAY DIFFRACTION84
3.6035-3.88160.21121230.18253906X-RAY DIFFRACTION85
3.8816-4.27190.21381350.15034065X-RAY DIFFRACTION88
4.2719-4.88940.16761620.13694563X-RAY DIFFRACTION100
4.8894-6.15750.19941430.17234609X-RAY DIFFRACTION100
6.1575-44.26560.24341330.20274567X-RAY DIFFRACTION99
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)
14.52942.5846-1.33596.203-2.45972.93720.1999-0.2308-0.36780.6435-0.09790.10390.1478-0.1125-0.12790.638-0.10210.07330.2860.02810.41235.2931-31.8446-26.2983
22.09111.489-0.34083.4277-0.64462.45720.11830.0064-0.02250.3362-0.07610.17730.0934-0.2897-0.06730.264-0.00230.05940.1976-0.00920.260910.0597-7.6326-38.4453
34.17122.72330.91016.63361.68982.44250.2932-0.4270.53490.5878-0.1747-0.0988-0.07280.0611-0.0980.7074-0.1782-0.15260.39320.00140.564235.739216.5691-23.582
41.16320.9874-0.12241.81780.28581.82250.1205-0.075-0.3110.5367-0.1405-0.72640.10210.37530.04250.4054-0.0128-0.1880.29390.06240.618134.8941-8.1805-33.7074
51.3070.12550.57681.8852-1.35292.48360.18220.72551.2304-0.6611-0.25280.3381-0.3483-0.38830.01740.85170.2952-0.07470.81530.37150.84086.24617.9883-77.2445
63.66420.16950.16853.34190.28971.86820.20740.5262-0.2221-0.2758-0.14240.15650.0933-0.1322-0.06580.29430.0888-0.02530.3346-0.03970.208115.8307-13.8883-64.6056
74.2963-1.6063-2.26863.81142.2172.69640.10970.8775-1.14420.3495-0.1109-0.25570.78680.54810.01590.78190.4360.0110.9543-0.16350.947251.1872-25.2275-69.5895
83.222-0.83550.02741.9483-0.35262.55910.26090.49930.3332-0.1836-0.1468-0.7897-0.05370.5163-0.11850.28590.05930.14070.43530.10320.489938.5214-4.4791-60.8623
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection details
1X-RAY DIFFRACTION1(chain A and resid 1:100)
2X-RAY DIFFRACTION2(chain A and resid 101:264)
3X-RAY DIFFRACTION3(chain B and resid 1:100)
4X-RAY DIFFRACTION4(chain B and resid 101:264)
5X-RAY DIFFRACTION5(chain C and resid 1:100)
6X-RAY DIFFRACTION6(chain C and resid 101:263)
7X-RAY DIFFRACTION7(chain D and resid 2:100)
8X-RAY DIFFRACTION8(chain D and resid 101:263)

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