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- PDB-4cp5: ndpK in complex with (Rp)-SPMPApp -

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Basic information

Entry
Database: PDB / ID: 4cp5
TitlendpK in complex with (Rp)-SPMPApp
ComponentsNUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC
KeywordsTRANSFERASE
Function / homology
Function and homology information


dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / negative regulation of pinocytosis / nucleoside triphosphate biosynthetic process / nucleoside-diphosphate kinase / UTP biosynthetic process ...dGTP biosynthetic process from dGDP / Azathioprine ADME / Ribavirin ADME / asexual reproduction / Interconversion of nucleotide di- and triphosphates / Neutrophil degranulation / negative regulation of pinocytosis / nucleoside triphosphate biosynthetic process / nucleoside-diphosphate kinase / UTP biosynthetic process / CTP biosynthetic process / negative regulation of exocytosis / GTP biosynthetic process / negative regulation of phagocytosis / nucleoside diphosphate kinase activity / translational elongation / phagocytic vesicle / secretory granule / response to bacterium / actin cytoskeleton organization / cytoskeleton / ribosome / G protein-coupled receptor signaling pathway / ATP binding / metal ion binding / plasma membrane / cytoplasm
Similarity search - Function
Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits ...Nucleoside diphosphate kinase (NDPK)-like domain profile. / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase, active site / Nucleoside diphosphate kinase (NDPK) active site signature. / Nucleoside diphosphate kinase / Nucleoside diphosphate kinase-like domain / Nucleoside diphosphate kinase / NDK / Nucleoside diphosphate kinase-like domain superfamily / Alpha-Beta Plaits / 2-Layer Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-EOI / Nucleoside diphosphate kinase, cytosolic
Similarity search - Component
Biological speciesDICTYOSTELIUM DISCOIDEUM (eukaryote)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.32 Å
AuthorsPriet, S. / Ferron, F. / Alvarez, K. / Verron, M. / Canard, B.
CitationJournal: Antiviral Res. / Year: 2015
Title: Enzymatic Synthesis of Acyclic Nucleoside Thiophosphonate Diphosphates: Effect of the Alpha-Phosphorus Configuration on HIV-1 RT Activity.
Authors: Priet, S. / Roux, L. / Saez-Ayala, M. / Ferron, F. / Canard, B. / Alvarez, K.
History
DepositionJan 31, 2014Deposition site: PDBE / Processing site: PDBE
Revision 1.0Feb 11, 2015Provider: repository / Type: Initial release
Revision 1.1Mar 25, 2015Group: Database references
Revision 1.2Apr 22, 2015Group: Database references
Revision 1.3Mar 4, 2020Group: Derived calculations / Other
Category: pdbx_database_status / pdbx_struct_assembly ...pdbx_database_status / pdbx_struct_assembly / pdbx_struct_assembly_gen / pdbx_struct_assembly_prop
Item: _pdbx_database_status.status_code_sf
Revision 1.4Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_initial_refinement_model / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _struct_site.pdbx_auth_asym_id / _struct_site.pdbx_auth_comp_id / _struct_site.pdbx_auth_seq_id

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Structure visualization

Structure viewerMolecule:
MolmilJmol/JSmol

Downloads & links

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Assembly

Deposited unit
A: NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC
B: NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC
C: NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC
D: NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC
E: NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC
F: NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)103,19112
Polymers100,4116
Non-polymers2,7796
Water9,098505
1


  • Idetical with deposited unit
  • defined by software
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12780 Å2
ΔGint-58 kcal/mol
Surface area35480 Å2
MethodPISA
Unit cell
Length a, b, c (Å)70.008, 105.790, 70.576
Angle α, β, γ (deg.)90.00, 117.23, 90.00
Int Tables number4
Space group name H-MP1211

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Components

#1: Protein
NUCLEOSIDE DIPHOSPHATE KINASE, CYTOSOLIC / NDK / NDP KINASE


Mass: 16735.242 Da / Num. of mol.: 6 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: S-PMPAPP / Source: (gene. exp.) DICTYOSTELIUM DISCOIDEUM (eukaryote) / Plasmid: PETG20A / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P22887, nucleoside-diphosphate kinase
#2: Chemical
ChemComp-EOI / [[(2R)-1-(6-aminopurin-9-yl)propan-2-yl]oxymethyl-sulfanyl-phosphoryl] phosphono hydrogen phosphate


Mass: 463.238 Da / Num. of mol.: 6 / Source method: obtained synthetically / Formula: C9H16N5O9P3S
#3: Water ChemComp-HOH / water


Mass: 18.015 Da / Num. of mol.: 505 / 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: 2.17 Å3/Da / Density % sol: 42.93 % / Description: NONE
Crystal growDetails: 26% PEG 1000 100MM TRIS PH7.5

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID29 / Wavelength: 1.00185
DetectorType: DECTRIS PILATUS 6M / Detector: PIXEL / Date: Oct 22, 2011 / Details: MIRRORS
RadiationMonochromator: SI (311) / Protocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 1.00185 Å / Relative weight: 1
ReflectionResolution: 2.32→33.43 Å / Num. obs: 38673 / % possible obs: 97.8 % / Observed criterion σ(I): -3 / Redundancy: 3.4 % / Biso Wilson estimate: 53.91 Å2 / Rmerge(I) obs: 0.06 / Net I/σ(I): 13.17
Reflection shellResolution: 2.32→2.4 Å / Redundancy: 3.5 % / Rmerge(I) obs: 0.49 / Mean I/σ(I) obs: 2.83 / % possible all: 96.6

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Processing

Software
NameVersionClassification
BUSTER2.11.5refinement
XDSdata reduction
SCALAdata scaling
PHASERphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 4C6A

4c6a


Resolution: 2.32→33.43 Å / Cor.coef. Fo:Fc: 0.891 / Cor.coef. Fo:Fc free: 0.8611 / SU R Cruickshank DPI: 0.45 / Cross valid method: THROUGHOUT / σ(F): 0 / SU R Blow DPI: 0.472 / SU Rfree Blow DPI: 0.254 / SU Rfree Cruickshank DPI: 0.255
Details: IDEAL-DIST CONTACT TERM CONTACT SETUP. ALL ATOMS HAVE CCP4 ATOM TYPE FROM LIBRARY
RfactorNum. reflection% reflectionSelection details
Rfree0.2463 1952 5.05 %RANDOM
Rwork0.1988 ---
obs0.2012 38673 97.65 %-
Displacement parametersBiso mean: 56.16 Å2
Baniso -1Baniso -2Baniso -3
1-18.2156 Å20 Å2-2.1766 Å2
2--13.2824 Å20 Å2
3----31.498 Å2
Refine analyzeLuzzati coordinate error obs: 0.345 Å
Refinement stepCycle: LAST / Resolution: 2.32→33.43 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms6900 0 162 505 7567
Refine LS restraints
Refine-IDTypeDev idealNumberRestraint functionWeight
X-RAY DIFFRACTIONt_bond_d0.017288HARMONIC2
X-RAY DIFFRACTIONt_angle_deg1.069912HARMONIC2
X-RAY DIFFRACTIONt_dihedral_angle_d2546SINUSOIDAL2
X-RAY DIFFRACTIONt_incorr_chiral_ct
X-RAY DIFFRACTIONt_pseud_angle
X-RAY DIFFRACTIONt_trig_c_planes161HARMONIC2
X-RAY DIFFRACTIONt_gen_planes1152HARMONIC5
X-RAY DIFFRACTIONt_it7288HARMONIC20
X-RAY DIFFRACTIONt_nbd
X-RAY DIFFRACTIONt_omega_torsion2.95
X-RAY DIFFRACTIONt_other_torsion15.68
X-RAY DIFFRACTIONt_improper_torsion
X-RAY DIFFRACTIONt_chiral_improper_torsion905SEMIHARMONIC5
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_contact8722SEMIHARMONIC4
LS refinement shellResolution: 2.32→2.38 Å / Total num. of bins used: 19
RfactorNum. reflection% reflection
Rfree0.4054 136 4.71 %
Rwork0.2686 2754 -
all0.2749 2890 -
obs--97.65 %

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