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- PDB-4o1l: Human Adenosine Kinase in complex with inhibitor -

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Basic information

Entry
Database: PDB / ID: 4o1l
TitleHuman Adenosine Kinase in complex with inhibitor
ComponentsAdenosine kinase
KeywordsTransferase/Transferase inhibitor / Adenosine Kinase / Transferase-Transferase inhibitor complex
Function / homology
Function and homology information


dATP biosynthetic process / adenosine kinase / adenosine kinase activity / dAMP salvage / ribonucleoside monophosphate biosynthetic process / deoxyadenosine kinase activity / Ribavirin ADME / GMP salvage / Purine salvage / AMP salvage ...dATP biosynthetic process / adenosine kinase / adenosine kinase activity / dAMP salvage / ribonucleoside monophosphate biosynthetic process / deoxyadenosine kinase activity / Ribavirin ADME / GMP salvage / Purine salvage / AMP salvage / purine ribonucleoside salvage / purine nucleobase metabolic process / phosphorylation / RNA binding / nucleoplasm / ATP binding / metal ion binding / nucleus / plasma membrane / cytosol
Similarity search - Function
Adenosine kinase / Adenosine kinase, small domain - #10 / Adenosine kinase, small domain / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase ...Adenosine kinase / Adenosine kinase, small domain - #10 / Adenosine kinase, small domain / pfkB family of carbohydrate kinases signature 2. / Carbohydrate/purine kinase, PfkB, conserved site / Carbohydrate kinase PfkB / pfkB family carbohydrate kinase / Ribokinase / Ribokinase-like / UDP-N-acetylmuramoyl-L-alanine:D-glutamate ligase / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
Chem-HO4 / Adenosine kinase
Similarity search - Component
Biological speciesHomo sapiens (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / molecular replacement / Resolution: 2.5 Å
AuthorsBrynda, J. / Dostal, J. / Pichova, I. / Hodcek, M.
CitationJournal: J.Med.Chem. / Year: 2014
Title: Structural Basis for Inhibition of Mycobacterial and Human Adenosine Kinase by 7-Substituted 7-(Het)aryl-7-deazaadenine Ribonucleosides
Authors: Snasel, J. / Naus, P. / Dostal, J. / Hnizda, A. / Fanfrlik, J. / Brynda, J. / Bourderioux, A. / Dusek, M. / Dvorakova, H. / Stolarikova, J. / Zabranska, H. / Pohl, R. / Konecny, P. / Dzubak, ...Authors: Snasel, J. / Naus, P. / Dostal, J. / Hnizda, A. / Fanfrlik, J. / Brynda, J. / Bourderioux, A. / Dusek, M. / Dvorakova, H. / Stolarikova, J. / Zabranska, H. / Pohl, R. / Konecny, P. / Dzubak, P. / Votruba, I. / Hajduch, M. / Rezacova, P. / Veverka, V. / Hocek, M. / Pichova, I.
History
DepositionDec 16, 2013Deposition site: RCSB / Processing site: PDBJ
Revision 1.0Nov 26, 2014Provider: repository / Type: Initial release
Revision 1.1Mar 20, 2024Group: 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_struct_conn_angle / struct_conn / struct_ncs_dom_lim / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _struct_conn.ptnr1_auth_asym_id / _struct_conn.ptnr1_auth_comp_id / _struct_conn.ptnr1_auth_seq_id / _struct_conn.ptnr1_label_asym_id / _struct_conn.ptnr1_label_atom_id / _struct_conn.ptnr1_label_comp_id / _struct_conn.ptnr1_label_seq_id / _struct_conn.ptnr2_auth_asym_id / _struct_conn.ptnr2_auth_comp_id / _struct_conn.ptnr2_auth_seq_id / _struct_conn.ptnr2_label_asym_id / _struct_conn.ptnr2_label_atom_id / _struct_conn.ptnr2_label_comp_id / _struct_ncs_dom_lim.beg_auth_comp_id / _struct_ncs_dom_lim.beg_label_asym_id / _struct_ncs_dom_lim.beg_label_comp_id / _struct_ncs_dom_lim.beg_label_seq_id / _struct_ncs_dom_lim.end_auth_comp_id / _struct_ncs_dom_lim.end_label_asym_id / _struct_ncs_dom_lim.end_label_comp_id / _struct_ncs_dom_lim.end_label_seq_id / _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: Adenosine kinase
B: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)78,6039
Polymers77,6352
Non-polymers9687
Water73941
1


  • Idetical with deposited unit
  • defined by author
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
2
A: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,4465
Polymers38,8171
Non-polymers6294
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
3
B: Adenosine kinase
hetero molecules


Theoretical massNumber of molelcules
Total (without water)39,1564
Polymers38,8171
Non-polymers3393
Water181
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
MethodPISA
Unit cell
Length a, b, c (Å)67.310, 156.590, 58.210
Angle α, β, γ (deg.)90.000, 90.000, 90.000
Int Tables number18
Space group name H-MP21212
Noncrystallographic symmetry (NCS)NCS domain:
IDEns-IDDetails
11A
21B

NCS domain segments:

Component-ID: 0 / Ens-ID: 1 / Beg auth comp-ID: LEU / Beg label comp-ID: LEU / End auth comp-ID: ILE / End label comp-ID: ILE / Refine code: 0 / Auth seq-ID: 4 - 330 / Label seq-ID: 5 - 331

Dom-IDAuth asym-IDLabel asym-ID
1AA
2BB

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Components

#1: Protein Adenosine kinase / / AK / Adenosine 5'-phosphotransferase


Mass: 38817.270 Da / Num. of mol.: 2 / Fragment: UNP residues 17-362
Source method: isolated from a genetically manipulated source
Source: (gene. exp.) Homo sapiens (human) / Gene: ADK / Production host: Escherichia coli (E. coli) / References: UniProt: P55263, adenosine kinase
#2: Chemical
ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 4 / Source method: obtained synthetically / Formula: Mg
#3: Chemical ChemComp-HO4 / 5-ethynyl-7-(beta-D-ribofuranosyl)-7H-pyrrolo[2,3-d]pyrimidin-4-amine


Mass: 290.275 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: C13H14N4O4
#4: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 41 / 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: 1.98 Å3/Da / Density % sol: 37.74 % / Mosaicity: 0.72 °

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: BESSY / Beamline: 14.1 / Wavelength: 0.91502 Å
DetectorType: MARMOSAIC 225 mm CCD / Detector: CCD / Date: Jun 2, 2011
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.91502 Å / Relative weight: 1
ReflectionResolution: 2.5→156.59 Å / Num. all: 22043 / Num. obs: 22043 / % possible obs: 99.9 % / Redundancy: 4.7 % / Rsym value: 0.08 / Net I/σ(I): 10.9
Reflection shell

Diffraction-ID: 1

Resolution (Å)Redundancy (%)Rmerge(I) obsMean I/σ(I) obsNum. measured allNum. unique allRpim(I) allRsym valueNet I/σ(I) obs% possible all
2.5-2.644.50.2622.91413131430.1540.2624.5100
2.64-2.84.70.2063.61414930210.120.2065.6100
2.8-2.994.80.1415.31340928030.0810.1417.6100
2.99-3.234.80.0977.71265026400.0560.0979.9100
3.23-3.544.80.06910.31170224350.0390.06913.2100
3.54-3.954.80.05612.61054122180.0310.05615.4100
3.95-4.564.70.05511.7928619650.030.05516.9100
4.56-5.594.60.0678.6786616990.0360.06716.5100
5.59-7.914.50.05410.6601513290.0310.0541599.8
7.91-52.1974.20.04710.232877900.0270.04718.498.8

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Phasing

PhasingMethod: molecular replacement
Phasing MR
Highest resolutionLowest resolution
Rotation3.5 Å51.04 Å
Translation3.5 Å51.04 Å

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Processing

Software
NameVersionClassificationNB
MOSFLMdata reduction
SCALA3.3.16data scaling
MOLREPphasing
REFMACrefinement
PDB_EXTRACT3.14data extraction
RefinementMethod to determine structure: MOLECULAR REPLACEMENT / Resolution: 2.5→156.59 Å / Cor.coef. Fo:Fc: 0.93 / Cor.coef. Fo:Fc free: 0.869 / SU B: 11.615 / SU ML: 0.272 / Cross valid method: THROUGHOUT / ESU R Free: 0.339 / Stereochemistry target values: MAXIMUM LIKELIHOOD / Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS
RfactorNum. reflection% reflectionSelection details
Rfree0.2628 1128 5.1 %RANDOM
Rwork0.19611 ---
obs0.19962 20803 99.57 %-
Solvent computationIon probe radii: 0.8 Å / Shrinkage radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: BABINET MODEL WITH MASK
Displacement parametersBiso mean: 33.362 Å2
Baniso -1Baniso -2Baniso -3
1-1.46 Å20 Å20 Å2
2---0.87 Å20 Å2
3----0.59 Å2
Refinement stepCycle: LAST / Resolution: 2.5→156.59 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms5214 0 67 41 5322
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0150.025384
X-RAY DIFFRACTIONr_bond_other_d0.0050.023630
X-RAY DIFFRACTIONr_angle_refined_deg1.6581.9667270
X-RAY DIFFRACTIONr_angle_other_deg1.3033.0048884
X-RAY DIFFRACTIONr_dihedral_angle_1_deg6.0855661
X-RAY DIFFRACTIONr_dihedral_angle_2_deg41.45125246
X-RAY DIFFRACTIONr_dihedral_angle_3_deg18.04415948
X-RAY DIFFRACTIONr_dihedral_angle_4_deg18.8741521
X-RAY DIFFRACTIONr_chiral_restr0.0890.2811
X-RAY DIFFRACTIONr_gen_planes_refined0.0070.025939
X-RAY DIFFRACTIONr_gen_planes_other0.0050.021067
X-RAY DIFFRACTIONr_nbd_refined
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it
X-RAY DIFFRACTIONr_scangle_other
X-RAY DIFFRACTIONr_long_range_B_refined
X-RAY DIFFRACTIONr_long_range_B_other
X-RAY DIFFRACTIONr_rigid_bond_restr
X-RAY DIFFRACTIONr_sphericity_free
X-RAY DIFFRACTIONr_sphericity_bonded
Refine LS restraints NCS

Ens-ID: 1 / Number: 11549 / Refine-ID: X-RAY DIFFRACTION / Type: interatomic distance / Rms dev position: 0.14 Å / Weight position: 0.05

Dom-IDAuth asym-ID
1A
2B
LS refinement shellResolution: 2.5→2.565 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.339 74 -
Rwork0.217 1366 -
obs--99.72 %

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