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- PDB-8oov: human NME-1 in complex with CoA -

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Basic information

Entry
Database: PDB / ID: 8oov
Titlehuman NME-1 in complex with CoA
ComponentsNucleoside diphosphate kinase A
KeywordsTRANSFERASE / nucleoside diphosphate kinase
Function / homology
Function and homology information


farnesyl-diphosphate kinase / farnesyl diphosphate kinase activity / succinyl-CoA binding / ITP biosynthetic process / isoprenoid metabolic process / Hydrolases; Acting on ester bonds; Site specific endodeoxyribonucleases: cleavage is not sequence specific (deleted sub-subclass) / DNA nuclease activity / phosphotransferase activity, phosphate group as acceptor / acetyl-CoA catabolic process / nucleoside triphosphate biosynthetic process ...farnesyl-diphosphate kinase / farnesyl diphosphate kinase activity / succinyl-CoA binding / ITP biosynthetic process / isoprenoid metabolic process / Hydrolases; Acting on ester bonds; Site specific endodeoxyribonucleases: cleavage is not sequence specific (deleted sub-subclass) / DNA nuclease activity / phosphotransferase activity, phosphate group as acceptor / acetyl-CoA catabolic process / nucleoside triphosphate biosynthetic process / acetyl-CoA binding / nucleoside diphosphate metabolic process / Ribavirin ADME / coenzyme A binding / protein histidine kinase activity / regulation of fatty acid biosynthetic process / apoptotic DNA fragmentation / nucleoside-diphosphate kinase / 3'-5'-DNA exonuclease activity / Interconversion of nucleotide di- and triphosphates / UTP biosynthetic process / CTP biosynthetic process / protein hexamerization / DNA catabolic process / Azathioprine ADME / nucleoside diphosphate kinase activity / GTP biosynthetic process / Hydrolases; Acting on ester bonds; Exodeoxyribonucleases producing 5'-phosphomonoesters / histidine kinase / ribosomal small subunit binding / lactation / positive regulation of epithelial cell proliferation / DNA endonuclease activity / ADP binding / ruffle membrane / endocytosis / kinase activity / GDP binding / nervous system development / regulation of apoptotic process / early endosome / cell differentiation / non-specific serine/threonine protein kinase / negative regulation of cell population proliferation / magnesium ion binding / DNA binding / RNA binding / extracellular exosome / ATP binding / membrane / identical protein binding / nucleus / 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
3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE / Nucleoside diphosphate kinase A
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 1.7 Å
AuthorsGouge, J. / Hristov, H.D.
Funding support United Kingdom, 3items
OrganizationGrant numberCountry
Wellcome Trust216404/A/19/Z United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/L010410/1 United Kingdom
Biotechnology and Biological Sciences Research Council (BBSRC)BB/S009027/1 United Kingdom
CitationJournal: Int J Mol Sci / Year: 2023
Title: A Unique Mode of Coenzyme A Binding to the Nucleotide Binding Pocket of Human Metastasis Suppressor NME1.
Authors: Tossounian, M.A. / Hristov, S.D. / Semelak, J.A. / Yu, B.Y.K. / Baczynska, M. / Zhao, Y. / Estrin, D.A. / Trujillo, M. / Filonenko, V. / Gouge, J. / Gout, I.
History
DepositionApr 6, 2023Deposition site: PDBE / Processing site: PDBE
Revision 1.0Jun 7, 2023Provider: repository / Type: Initial release
Revision 1.1Jun 21, 2023Group: Database references / Category: citation / citation_author
Item: _citation.journal_volume / _citation.pdbx_database_id_PubMed ..._citation.journal_volume / _citation.pdbx_database_id_PubMed / _citation.title / _citation_author.name
Revision 1.2Jun 19, 2024Group: Data collection / Category: chem_comp_atom / chem_comp_bond

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: Nucleoside diphosphate kinase A
B: Nucleoside diphosphate kinase A
C: Nucleoside diphosphate kinase A
hetero molecules


Theoretical massNumber of molelcules
Total (without water)59,6667
Polymers58,0263
Non-polymers1,6404
Water9,224512
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area7400 Å2
ΔGint-23 kcal/mol
Surface area20820 Å2
Unit cell
Length a, b, c (Å)79.070, 113.012, 118.119
Angle α, β, γ (deg.)90.00, 90.00, 90.00
Int Tables number24
Space group name H-MI212121
Components on special symmetry positions
IDModelComponents
11B-449-

HOH

21B-473-

HOH

31B-474-

HOH

41C-471-

HOH

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Components

#1: Protein Nucleoside diphosphate kinase A / NDK A / NDP kinase A / Granzyme A-activated DNase / GAAD / Metastasis inhibition factor nm23 / NM23- ...NDK A / NDP kinase A / Granzyme A-activated DNase / GAAD / Metastasis inhibition factor nm23 / NM23-H1 / Tumor metastatic process-associated protein


Mass: 19342.090 Da / Num. of mol.: 3
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: NME1, NDPKA, NM23 / Production host: Escherichia coli (E. coli) / References: UniProt: P15531, nucleoside-diphosphate kinase
#2: Chemical ChemComp-PAP / 3'-PHOSPHATE-ADENOSINE-5'-DIPHOSPHATE


Mass: 507.181 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C10H16N5O13P3 / Feature type: SUBJECT OF INVESTIGATION
#3: Chemical ChemComp-MPD / (4S)-2-METHYL-2,4-PENTANEDIOL


Mass: 118.174 Da / Num. of mol.: 1 / Source method: obtained synthetically / Formula: C6H14O2 / Comment: precipitant*YM
#4: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 512 / Source method: isolated from a natural source / Formula: H2O
Has ligand of interestY

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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: 2.27 Å3/Da / Density % sol: 45.9 %
Crystal growTemperature: 293 K / Method: vapor diffusion, hanging drop / Details: 28% MPD, 100mM MES pH 6.5

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Data collection

DiffractionMean temperature: 100 K / Serial crystal experiment: N
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: MASSIF-1 / Wavelength: 0.965459 Å
DetectorType: DECTRIS PILATUS3 2M / Detector: PIXEL / Date: Sep 18, 2020
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.965459 Å / Relative weight: 1
ReflectionResolution: 1.7→43.65 Å / Num. obs: 58147 / % possible obs: 99.6 % / Redundancy: 5 % / CC1/2: 0.996 / Rmerge(I) obs: 0.099 / Net I/σ(I): 9.2
Reflection shellResolution: 1.7→1.73 Å / Rmerge(I) obs: 1.081 / Num. unique obs: 3052 / CC1/2: 0.505

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Processing

Software
NameVersionClassification
BUSTER2.10.4 (21-NOV-2022)refinement
XDSdata reduction
Aimlessdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 1.7→23.66 Å / Cor.coef. Fo:Fc: 0.965 / Cor.coef. Fo:Fc free: 0.953 / SU R Cruickshank DPI: 0.095 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.102 / SU Rfree Blow DPI: 0.096 / SU Rfree Cruickshank DPI: 0.092
RfactorNum. reflection% reflectionSelection details
Rfree0.1959 2949 5.08 %RANDOM
Rwork0.1681 ---
obs0.1695 58098 99.5 %-
Displacement parametersBiso mean: 27.14 Å2
Baniso -1Baniso -2Baniso -3
1-2.1547 Å20 Å20 Å2
2--1.8975 Å20 Å2
3----4.0522 Å2
Refine analyzeLuzzati coordinate error obs: 0.19 Å
Refinement stepCycle: LAST / Resolution: 1.7→23.66 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms3694 0 101 523 4318
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.0094037HARMONIC2
X-RAY DIFFRACTIONt_angle_deg0.975497HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d1457SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes
X-RAY DIFFRACTIONt_gen_planes706HARMONIC5
X-RAY DIFFRACTIONt_it4037HARMONIC10
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion3.86
X-RAY DIFFRACTIONt_other_torsion13.3
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion496SEMIHARMONIC5
X-RAY DIFFRACTIONt_sum_occupancies
X-RAY DIFFRACTIONt_utility_distance
X-RAY DIFFRACTIONt_utility_angle
X-RAY DIFFRACTIONt_utility_torsion
X-RAY DIFFRACTIONt_ideal_dist_contact4180SEMIHARMONIC4
LS refinement shellResolution: 1.7→1.71 Å / Total num. of bins used: 51
RfactorNum. reflection% reflection
Rfree0.3226 -4.99 %
Rwork0.2809 1104 -
all0.2828 1162 -
obs--99.74 %
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)
11.6884-0.07390.13260-0.31432.6712-0.0169-0.3380.06580.16280.025-0.0374-0.11570.0365-0.00810.17230.09670.0633-0.01420.11160.0618-3.815123.262121.1959
20.27290.164-0.04150-0.22590.2267-0.00610.01520.02280.020.00070.021-0.02350.01720.0053-0.0160.0035-0.0016-0.0082-0.01160.012721.182525.343111.4916
30.31690.22740.16350.35550.18010.2084-0.0217-0.04810.02610.0337-0.00640.01970.0121-0.02050.0281-0.01670.00690.005-0.0104-0.00940.005315.485321.347312.834
40.09420.23430.07431.12010.082900.0322-0.02170.0146-0.0209-0.0312-0.05250.030.0066-0.0010.00720.0147-0.0089-0.01210.0034-0.003833.9768-3.070910.0813
52.35360.1269-1.52771.0272-0.74922.10520.0445-0.1159-0.0817-0.0155-0.0182-0.04280.03270.0033-0.02630.01410.0241-0.0109-0.04130.0237-0.016234.2241-20.386220.8865
60.0696-0.0905-0.05320.706-0.36880.2224-0.0159-0.03680.00730.0397-0.0051-0.02110.02640.02030.0210.01280.0172-0.0208-0.02180.0015-0.012333.2332-3.449715.0757
70.3149-0.46390.45440.8556-0.24550.42730.01750.0409-0.00150.0441-0.02090.02540.063-0.04070.00340.0081-0.02020.003-0.01710.005-0.00474.6713-5.57774.9225
83.834-0.855-2.34562.08542.88456.76870.0704-0.1448-0.27320.1435-0.02720.40250.1569-0.2832-0.0432-0.1249-0.07650.10410.0380.00250.0227-13.6536-0.557112.0697
90.4992-0.2785-0.00460.27380.1570.35030.0119-0.0527-0.00860.0841-0.01340.0260.0625-0.08810.0014-0.0021-0.0250.0252-0.01180.0172-0.00521.7887-4.047410.2856
Refinement TLS group
IDRefine-IDRefine TLS-IDSelection detailsAuth asym-IDAuth seq-ID
1X-RAY DIFFRACTION1{ B|-4 - B|-2 }B-4 - -2
2X-RAY DIFFRACTION2{ B|-1 - B|81 }B-1 - 81
3X-RAY DIFFRACTION3{ B|82 - B|152 }B82 - 152
4X-RAY DIFFRACTION4{ C|2 - C|41 }C2 - 41
5X-RAY DIFFRACTION5{ C|42 - C|66 }C42 - 66
6X-RAY DIFFRACTION6{ C|67 - C|152 }C67 - 152
7X-RAY DIFFRACTION7{ A|1 - A|41 }A1 - 41
8X-RAY DIFFRACTION8{ A|42 - A|58 }A42 - 58
9X-RAY DIFFRACTION9{ A|59 - A|152 }A59 - 152

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