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

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Basic information

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


NAD+ kinase / NAD+ kinase activity / NADP+ biosynthetic process / NAD+ metabolic process / NAD binding / 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 / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / 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 / NAD kinase/diacylglycerol kinase-like domain superfamily / Inorganic polyphosphate/ATP-NAD kinase, N-terminal / Tumour Suppressor Smad4 / Sandwich / Rossmann fold / 3-Layer(aba) Sandwich / Mainly Beta / Alpha Beta
Similarity search - Domain/homology
Chem-5A9 / CITRIC ACID / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.59 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)127,00712
Polymers124,1814
Non-polymers2,8268
Water3,387188
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10550 Å2
ΔGint-42 kcal/mol
Surface area40320 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.781, 119.072, 67.347
Angle α, β, γ (deg.)90.00, 100.03, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NAD kinase 1 / 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)
Strain: ATCC BAA-679 / EGD-e / Gene: nadK1, lmo0968 / Production host: Escherichia coli (E. coli) / References: UniProt: Q8Y8D7, NAD+ kinase
#2: Chemical ChemComp-CIT / CITRIC ACID


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


Mass: 92.094 Da / Num. of mol.: 2 / Source method: obtained synthetically / Formula: C3H8O3
#4: Chemical
ChemComp-5A9 / 5'-azido-8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]-5'-deoxyadenosine


Mass: 564.416 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H22BrN9O4S
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 188 / 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: 2.12 Å3/Da / Density % sol: 42.07 %
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: Jul 11, 2012
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.9334 Å / Relative weight: 1
ReflectionResolution: 2.59→66.317 Å / Num. all: 32287 / Num. obs: 32287 / % possible obs: 99.9 % / Redundancy: 2.8 % / Biso Wilson estimate: 50.88 Å2 / Rpim(I) all: 0.032 / Rrim(I) all: 0.052 / Rsym value: 0.035 / Net I/av σ(I): 19.333 / Net I/σ(I): 16.9 / Num. measured all: 89093
Reflection shell

Diffraction-ID: 1 / Rejects: _

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.59-2.732.80.352.21318146960.2870.352.6100
2.73-2.92.80.2423.21243744380.2030.2423.6100
2.9-3.12.80.155.21157441810.1270.155.6100
3.1-3.342.80.0829.61076839130.070.0829.7100
3.34-3.662.70.04216.1947735660.0390.04216.999.9
3.66-4.12.60.02823.1846532410.0270.02824.499.5
4.1-4.732.80.01739.3808928720.0150.01734.8100
4.73-5.792.90.01643692724220.0130.01638100
5.79-8.192.80.01546.5535818990.0130.01539.4100
8.19-66.3172.70.01340.5281710590.0120.01347.999.7

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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: 2.59→66.317 Å / SU ML: 0.41 / Cross valid method: FREE R-VALUE / σ(F): 0.01 / Phase error: 31.14 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.2714 1973 3.12 %
Rwork0.2292 --
obs0.2305 63300 99.61 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.59→66.317 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8109 0 178 188 8475
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0058491
X-RAY DIFFRACTIONf_angle_d0.69511493
X-RAY DIFFRACTIONf_dihedral_angle_d11.0193049
X-RAY DIFFRACTIONf_chiral_restr0.0291247
X-RAY DIFFRACTIONf_plane_restr0.0031466
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.59-2.65480.42441090.36674352X-RAY DIFFRACTION100
2.6548-2.72660.40251550.34194422X-RAY DIFFRACTION100
2.7266-2.80680.31511300.32354416X-RAY DIFFRACTION100
2.8068-2.89740.38151370.31734384X-RAY DIFFRACTION100
2.8974-3.00090.34871350.29294367X-RAY DIFFRACTION100
3.0009-3.12110.2951700.27094364X-RAY DIFFRACTION100
3.1211-3.26310.25661250.24894432X-RAY DIFFRACTION100
3.2631-3.43520.28611620.23894379X-RAY DIFFRACTION100
3.4352-3.65040.27181630.23324307X-RAY DIFFRACTION99
3.6504-3.93220.32811270.27694365X-RAY DIFFRACTION98
3.9322-4.32780.22181530.1834353X-RAY DIFFRACTION100
4.3278-4.95390.21611380.14814401X-RAY DIFFRACTION100
4.9539-6.24070.21281380.18774386X-RAY DIFFRACTION100
6.2407-66.33850.25571310.20644399X-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)
15.00953.3928-1.52825.641-1.79272.69020.1996-0.2844-0.30980.7958-0.1847-0.080.3795-0.0707-0.00760.7812-0.09930.08320.36780.01440.47285.2576-32.5323-26.2841
23.26151.0227-0.75414.3051-1.01673.67690.1408-0.00720.02190.3745-0.09690.26870.1454-0.2864-0.07090.3559-0.050.06130.2478-0.05730.29619.9395-8.65-38.616
33.67130.07151.37593.672.67133.450.5197-0.54931.05950.4822-0.3409-0.444-0.38430.4154-0.10340.8752-0.3615-0.05830.6415-0.08270.792835.932415.4513-24.1016
42.8315-0.5095-0.20783.9151.03673.22250.0705-0.2873-0.44680.6395-0.0415-0.6040.26430.5942-0.00660.456-0.0572-0.14180.44130.09280.591434.5765-9.2696-34.2275
53.2832-1.17981.61854.6877-2.17843.91930.10170.99031.2504-0.7866-0.05860.6331-0.3654-0.2544-0.010.85750.1962-0.07510.82990.33120.94076.00366.8606-77.3073
64.26250.5154-0.17544.5247-0.34222.65760.09930.6332-0.2859-0.463-0.08260.23710.1371-0.2483-0.01570.41660.12460.00090.4449-0.07450.278315.3757-15.0209-64.7046
74.9746-0.9574-2.29223.38823.43573.88120.28190.388-0.4381-0.0399-0.0541-0.8430.6831.0659-0.15770.87940.41060.17690.9805-0.07591.00551.1665-26.8589-69.7609
83.2628-0.4407-0.05112.88860.21332.77880.21610.56050.2891-0.3924-0.1037-0.8091-0.05970.486-0.15090.33770.0510.11020.49630.07860.512938.0268-5.4827-61.0987
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 101:264)
7X-RAY DIFFRACTION7(chain D and resid 1:100)
8X-RAY DIFFRACTION8(chain D and resid 101:264)

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