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

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Basic information

Entry
Database: PDB / ID: 5dhq
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-5AK / CITRIC ACID / NAD kinase 1
Similarity search - Component
Biological speciesListeria monocytogenes serovar 1/2a (bacteria)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.29 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)126,81511
Polymers124,1814
Non-polymers2,6347
Water3,567198
1


  • Idetical with deposited unit
  • defined by author&software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area10510 Å2
ΔGint-45 kcal/mol
Surface area39880 Å2
MethodPISA
Unit cell
Length a, b, c (Å)66.790, 119.180, 67.210
Angle α, β, γ (deg.)90.00, 99.91, 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)
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-5AK / 8-[(2-{[2-(3-bromophenyl)ethyl]amino}-2-oxoethyl)sulfanyl]adenosine


Mass: 539.403 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: C20H23BrN6O5S
#4: Chemical ChemComp-GOL / GLYCEROL / GLYCERIN / PROPANE-1,2,3-TRIOL


Mass: 92.094 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C3H8O3
#5: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 198 / 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: 42.03 %
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: 2.29→66.207 Å / Num. all: 43420 / Num. obs: 43420 / % possible obs: 93.1 % / Redundancy: 3 % / Biso Wilson estimate: 36.64 Å2 / Rpim(I) all: 0.029 / Rrim(I) all: 0.051 / Rsym value: 0.035 / Net I/av σ(I): 15.897 / Net I/σ(I): 20.1 / Num. measured all: 128384
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
2.29-2.413.10.4431.32094867890.3540.4432.7100
2.41-2.563.10.3581.61999764310.2810.3583.4100
2.56-2.7430.2452.41424746760.1970.2454.777.6
2.74-2.962.90.14641651456280.1190.1467.1100
2.96-3.242.80.0698.91469451600.0580.06913.2100
3.24-3.622.80.0321.61146941120.0250.0324.987.5
3.62-4.182.80.01542799828800.0130.01540.969.1
4.18-5.122.90.0156.21031735130.0080.0161100
5.12-7.242.80.01152.1750127140.0090.01157.9100
7.24-44.2923.10.00950.8469915170.0060.00971.899.5

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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: 2.29→44.292 Å / SU ML: 0.57 / Cross valid method: FREE R-VALUE / σ(F): 0 / Phase error: 41.9 / Stereochemistry target values: ML
RfactorNum. reflection% reflection
Rfree0.3106 2505 3.03 %
Rwork0.26 --
obs0.2616 41997 89.94 %
Solvent computationShrinkage radii: 0.9 Å / VDW probe radii: 1.11 Å / Solvent model: FLAT BULK SOLVENT MODEL
Refinement stepCycle: LAST / Resolution: 2.29→44.292 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms8120 0 164 198 8482
Refine LS restraints
Refine-IDTypeDev idealNumber
X-RAY DIFFRACTIONf_bond_d0.0068488
X-RAY DIFFRACTIONf_angle_d0.60111493
X-RAY DIFFRACTIONf_dihedral_angle_d10.853081
X-RAY DIFFRACTIONf_chiral_restr0.0241252
X-RAY DIFFRACTIONf_plane_restr0.0021461
LS refinement shell
Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRefine-ID% reflection obs (%)
2.29-2.3340.50831210.52484616X-RAY DIFFRACTION92
2.334-2.38170.50431340.50134647X-RAY DIFFRACTION93
2.3817-2.43350.53961610.50154509X-RAY DIFFRACTION93
2.4335-2.49010.53461600.45974731X-RAY DIFFRACTION94
2.4901-2.55230.46741490.44344586X-RAY DIFFRACTION95
2.5523-2.62130.47341260.40054786X-RAY DIFFRACTION95
2.6213-2.69850.3508620.39222248X-RAY DIFFRACTION45
2.6985-2.78560.44611340.35384863X-RAY DIFFRACTION97
2.7856-2.88510.35981490.32414774X-RAY DIFFRACTION97
2.8851-3.00060.36291380.30474813X-RAY DIFFRACTION98
3.0006-3.13710.31921790.28024834X-RAY DIFFRACTION99
3.1371-3.30250.31831410.25194914X-RAY DIFFRACTION99
3.3025-3.50930.3031480.22033843X-RAY DIFFRACTION77
3.5093-3.78010.36821100.21373439X-RAY DIFFRACTION70
3.7801-4.16030.20111210.17993760X-RAY DIFFRACTION76
4.1603-4.76160.20261670.14874948X-RAY DIFFRACTION100
4.7616-5.99680.22241570.17884934X-RAY DIFFRACTION100
5.9968-44.30.26211480.21944929X-RAY DIFFRACTION100
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)
13.08350.831-0.28383.9436-1.42321.91630.1175-0.1996-0.36970.7175-0.18730.0160.2746-0.03820.05690.7252-0.10420.08590.25820.00630.47895.1266-30.7875-26.1525
22.542.0716-0.74833.1187-0.75763.33970.1673-0.0096-0.07890.2931-0.07370.30680.1152-0.3216-0.120.3072-0.00650.02050.1881-0.04240.30959.8273-6.901-38.5117
33.40491.14560.73153.49911.26021.5940.353-0.76280.91430.4686-0.1322-0.3048-0.55720.4908-0.19270.9139-0.4161-0.01360.7645-0.11670.775235.758217.5004-24.1425
42.66460.725-0.36341.48080.13482.62540.1437-0.4662-0.33870.5081-0.1976-0.78830.10170.73390.01520.3875-0.0555-0.1960.44450.11350.688634.5009-7.3637-33.8965
52.6484-0.94291.50843.5623-2.67223.8740.23340.86441.0414-0.7107-0.11720.1692-0.5044-0.3173-0.0860.78580.24250.00940.83220.33480.85165.88178.4622-77.3264
64.4477-0.3124-0.23932.54980.68282.9020.11270.7334-0.5029-0.2203-0.1659-0.08350.2225-0.12670.04260.3390.1143-0.00450.3643-0.07570.282615.2189-13.3263-64.6078
74.8858-2.6935-2.41385.01932.953.46050.12210.8037-0.68430.1594-0.29240.13510.60170.59420.15820.65250.36770.10321.139-0.09230.911550.7832-24.5131-69.7008
83.1017-0.898-0.2341.04750.08482.06230.24390.43860.2181-0.1295-0.1185-0.9849-0.0680.449-0.13690.26280.07160.14180.51160.07680.602438.0412-3.682-60.9742
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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