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- PDB-8qw3: Human NDPK-C in complex with ADP -

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Basic information

Entry
Database: PDB / ID: 8qw3
TitleHuman NDPK-C in complex with ADP
ComponentsNucleoside diphosphate kinase 3
KeywordsTRANSFERASE / Kinase
Function / homology
Function and homology information


nucleoside triphosphate biosynthetic process / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / mitochondrial fusion / nucleoside diphosphate kinase activity / GTP biosynthetic process / mitochondrial outer membrane / ciliary basal body ...nucleoside triphosphate biosynthetic process / nucleoside-diphosphate kinase / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / mitochondrial fusion / nucleoside diphosphate kinase activity / GTP biosynthetic process / mitochondrial outer membrane / ciliary basal body / DNA repair / apoptotic process / mitochondrion / ATP binding / metal ion binding / cytoplasm / cytosol
Similarity search - Function
Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily
Similarity search - Domain/homology
ADENOSINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase 3
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.255 Å
AuthorsWerten, S. / Amjadi, R. / Scheffzek, K.
Funding support1items
OrganizationGrant numberCountry
Not funded
CitationJournal: Int J Mol Sci / Year: 2024
Title: Mechanistic Insights into Substrate Recognition of Human Nucleoside Diphosphate Kinase C Based on Nucleotide-Induced Structural Changes.
Authors: Amjadi, R. / Werten, S. / Lomada, S.K. / Baldin, C. / Scheffzek, K. / Dunzendorfer-Matt, T. / Wieland, T.
History
DepositionOct 18, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Sep 18, 2024Provider: repository / Type: Initial release
Revision 1.1Oct 9, 2024Group: Database references / Structure summary / Category: citation / pdbx_entry_details
Item: _citation.pdbx_database_id_PubMed / _citation.title / _pdbx_entry_details.has_protein_modification

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase 3
B: Nucleoside diphosphate kinase 3
C: Nucleoside diphosphate kinase 3
D: Nucleoside diphosphate kinase 3
E: Nucleoside diphosphate kinase 3
F: Nucleoside diphosphate kinase 3
hetero molecules


Theoretical massNumber of molelcules
Total (without water)108,12215
Polymers105,2716
Non-polymers2,8519
Water9,764542
1


  • Idetical with deposited unit
  • defined by author&software
  • Evidence: gel filtration
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area22670 Å2
ΔGint-141 kcal/mol
Surface area33130 Å2
MethodPISA
Unit cell
Length a, b, c (Å)52.315, 67.865, 68.423
Angle α, β, γ (deg.)108.492, 112.343, 101.105
Int Tables number1
Space group name H-MP1

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Components

#1: Protein
Nucleoside diphosphate kinase 3


Mass: 17545.137 Da / Num. of mol.: 6
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NME3 / Production host: Escherichia coli (E. coli) / References: UniProt: Q13232
#2: Chemical
ChemComp-ADP / ADENOSINE-5'-DIPHOSPHATE


Mass: 427.201 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C10H15N5O10P2 / Feature type: SUBJECT OF INVESTIGATION / Comment: ADP, energy-carrying molecule*YM
#3: Chemical ChemComp-SO4 / SULFATE ION


Mass: 96.063 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: SO4
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 542 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY
Has protein modificationN

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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: 1.89 Å3/Da / Density % sol: 35.1 %
Crystal growTemperature: 291 K / Method: vapor diffusion / pH: 5.4
Details: 6% PEG 3350, 150 mM Li2SO4, 100 mM Tri-sodium citrate pH 5.4

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-1 / Wavelength: 1.0052 Å
DetectorType: DECTRIS PILATUS 6M-F / Detector: PIXEL / Date: Dec 11, 2020 / Details: Toroidal mirror
RadiationMonochromator: Si(111) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.0052 Å / Relative weight: 1
ReflectionResolution: 1.25→60.12 Å / Num. obs: 198602 / % possible obs: 94.2 % / Redundancy: 2.8 % / Biso Wilson estimate: 12.8 Å2 / CC1/2: 0.97 / Rmerge(I) obs: 0.049 / Rpim(I) all: 0.033 / Rrim(I) all: 0.06 / Net I/σ(I): 8.6
Reflection shellResolution: 1.25→1.28 Å / Redundancy: 1.8 % / Rmerge(I) obs: 0.947 / Mean I/σ(I) obs: 0.7 / Num. unique obs: 9337 / CC1/2: 0.401 / Rpim(I) all: 0.947 / Rrim(I) all: 1.339 / % possible all: 89

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Processing

Software
NameVersionClassification
REFMAC5.8.0419refinement
MOSFLMdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.255→60.119 Å / Cor.coef. Fo:Fc: 0.978 / Cor.coef. Fo:Fc free: 0.972 / Cross valid method: FREE R-VALUE / ESU R: 0.048 / ESU R Free: 0.046
Details: Hydrogens have been added in their riding positions
RfactorNum. reflection% reflection
Rfree0.1755 2119 1.067 %
Rwork0.1467 196386 -
all0.147 --
obs-198505 94.108 %
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 19.87 Å2
Baniso -1Baniso -2Baniso -3
1--0.238 Å2-0.167 Å2-0.151 Å2
2---0.071 Å2-0.243 Å2
3---0.425 Å2
Refinement stepCycle: LAST / Resolution: 1.255→60.119 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms7253 0 177 542 7972
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0120.0127794
X-RAY DIFFRACTIONr_bond_other_d0.0020.0167308
X-RAY DIFFRACTIONr_angle_refined_deg1.6711.65410609
X-RAY DIFFRACTIONr_angle_other_deg0.9161.58216736
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.3785949
X-RAY DIFFRACTIONr_dihedral_angle_2_deg21.308594
X-RAY DIFFRACTIONr_dihedral_angle_other_2_deg1.35556
X-RAY DIFFRACTIONr_dihedral_angle_3_deg14.919101277
X-RAY DIFFRACTIONr_dihedral_angle_6_deg15.60910365
X-RAY DIFFRACTIONr_chiral_restr0.0960.21141
X-RAY DIFFRACTIONr_gen_planes_refined0.010.029505
X-RAY DIFFRACTIONr_gen_planes_other0.0130.021941
X-RAY DIFFRACTIONr_nbd_refined0.2240.21505
X-RAY DIFFRACTIONr_symmetry_nbd_other0.2080.26984
X-RAY DIFFRACTIONr_nbtor_refined0.1870.23789
X-RAY DIFFRACTIONr_symmetry_nbtor_other0.0830.24261
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.140.2443
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_other0.0570.21
X-RAY DIFFRACTIONr_symmetry_nbd_refined0.3890.231
X-RAY DIFFRACTIONr_nbd_other0.410.291
X-RAY DIFFRACTIONr_symmetry_xyhbond_nbd_refined0.1780.227
X-RAY DIFFRACTIONr_mcbond_it6.1481.8353757
X-RAY DIFFRACTIONr_mcbond_other6.1271.8353757
X-RAY DIFFRACTIONr_mcangle_it8.763.2944719
X-RAY DIFFRACTIONr_mcangle_other8.7613.2954720
X-RAY DIFFRACTIONr_scbond_it8.62.3154037
X-RAY DIFFRACTIONr_scbond_other8.62.3154037
X-RAY DIFFRACTIONr_scangle_it12.3254.0755890
X-RAY DIFFRACTIONr_scangle_other12.3244.0755891
X-RAY DIFFRACTIONr_lrange_it16.29322.8948894
X-RAY DIFFRACTIONr_lrange_other15.88422.3848812
X-RAY DIFFRACTIONr_rigid_bond_restr4.395315102
LS refinement shell

Refine-ID: X-RAY DIFFRACTION / Total num. of bins used: 20

Resolution (Å)Rfactor RfreeNum. reflection RfreeRfactor RworkNum. reflection RworkRfactor allNum. reflection allFsc freeFsc work% reflection obs (%)WRfactor Rwork
1.255-1.2880.2841600.338138190.337156480.9030.9289.33410.344
1.288-1.3230.3111350.307135790.308151610.9340.94190.45580.312
1.323-1.3610.2521340.291133070.291148090.9580.94990.76240.295
1.361-1.4030.2911300.263128380.264143830.9550.95790.1620.267
1.403-1.4490.2431650.236125940.236138910.9680.96691.85080.236
1.449-1.50.2391630.184123710.184134580.9710.9893.13420.174
1.5-1.5560.1781360.129121530.13130110.980.98994.45090.121
1.556-1.620.1651230.119116980.12124880.9840.99294.65890.111
1.62-1.6920.1811270.117112930.117120280.9810.99294.94510.109
1.692-1.7740.1571410.111108040.111114230.9860.99395.81550.104
1.774-1.870.1451030.104103370.105109100.9870.99495.6920.101
1.87-1.9840.1821060.10998630.11103200.9790.99396.59880.107
1.984-2.120.146880.10792380.10896540.9880.99396.60240.108
2.12-2.290.159860.11386960.11390390.9860.99297.15680.116
2.29-2.5080.138790.12180200.12183010.9850.99197.56660.125
2.508-2.8040.165570.13472830.13474860.9810.98998.04970.141
2.804-3.2360.175530.14164680.14266390.9840.98898.22260.155
3.236-3.9610.129530.13454470.13455720.9870.98998.70780.151
3.961-5.5890.15540.14442260.14443180.9840.98999.120.169
5.589-60.1190.254260.20323510.20323940.9680.96799.28990.234

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