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- PDB-2wvj: Mutation of Thr163 to Ser in Human Thymidine Kinase Shifts the Sp... -

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Basic information

Entry
Database: PDB / ID: 2wvj
TitleMutation of Thr163 to Ser in Human Thymidine Kinase Shifts the Specificity from Thymidine towards the Nucleoside Analogue Azidothymidine
ComponentsTHYMIDINE KINASE, CYTOSOLIC
KeywordsTRANSFERASE / ZINC-BINDING DOMAIN / DEOXYRIBONUCLEOSIDE KINASE / FEEDBACK INHIBITOR / NUCLEOTIDE-BINDING / KINASE / CYTOPLASM / ATP-BINDING / DNA SYNTHESIS / PHOSPHOPROTEIN / PHOSPHORYLATION
Function / homology
Function and homology information


DNA synthesis involved in mitotic DNA replication / thymidine biosynthetic process / thymidine metabolic process / thymidine kinase / thymidine kinase activity / Pyrimidine salvage / nucleobase-containing compound metabolic process / G1/S-Specific Transcription / protein homotetramerization / phosphorylation ...DNA synthesis involved in mitotic DNA replication / thymidine biosynthetic process / thymidine metabolic process / thymidine kinase / thymidine kinase activity / Pyrimidine salvage / nucleobase-containing compound metabolic process / G1/S-Specific Transcription / protein homotetramerization / phosphorylation / zinc ion binding / ATP binding / identical protein binding / nucleus / cytosol
Similarity search - Function
Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich ...Thymidine kinase / Thymidine kinase, conserved site / Thymidine kinase / Thymidine kinase cellular-type signature. / Wheat Germ Agglutinin (Isolectin 2); domain 1 - #20 / Wheat Germ Agglutinin (Isolectin 2); domain 1 / P-loop containing nucleotide triphosphate hydrolases / P-loop containing nucleoside triphosphate hydrolase / Rossmann fold / 2-Layer Sandwich / 3-Layer(aba) Sandwich / Alpha Beta
Similarity search - Domain/homology
THYMIDINE-5'-TRIPHOSPHATE / Thymidine kinase, cytosolic
Similarity search - Component
Biological speciesHOMO SAPIENS (human)
MethodX-RAY DIFFRACTION / SYNCHROTRON / MOLECULAR REPLACEMENT / Resolution: 2.2 Å
AuthorsSkovgaard, T. / Uhlin, U. / Munch-Petersen, B.
CitationJournal: FEBS J. / Year: 2012
Title: Comparative Active-Site Mutation Study of Human and Caenorhabditis Elegans Thymidine Kinase 1.
Authors: Skovgaard, T. / Uhlin, U. / Munch-Petersen, B.
History
DepositionOct 17, 2009Deposition site: PDBE / Processing site: PDBE
Revision 1.0Oct 27, 2009Provider: repository / Type: Initial release
Revision 1.1May 2, 2012Group: Database references / Derived calculations / Version format compliance
Revision 1.2May 8, 2019Group: Data collection / Experimental preparation / Other
Category: database_PDB_rev / database_PDB_rev_record ...database_PDB_rev / database_PDB_rev_record / exptl_crystal_grow / pdbx_database_proc / pdbx_database_status / pdbx_seq_map_depositor_info
Item: _exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval ..._exptl_crystal_grow.method / _pdbx_database_status.recvd_author_approval / _pdbx_seq_map_depositor_info.one_letter_code / _pdbx_seq_map_depositor_info.one_letter_code_mod
Revision 1.3Dec 20, 2023Group: Data collection / Database references ...Data collection / Database references / Derived calculations / Other / Refinement description
Category: chem_comp_atom / chem_comp_bond ...chem_comp_atom / chem_comp_bond / database_2 / pdbx_database_status / pdbx_initial_refinement_model / pdbx_struct_conn_angle / struct_conn / struct_site
Item: _database_2.pdbx_DOI / _database_2.pdbx_database_accession ..._database_2.pdbx_DOI / _database_2.pdbx_database_accession / _pdbx_database_status.status_code_sf / _pdbx_struct_conn_angle.ptnr1_auth_comp_id / _pdbx_struct_conn_angle.ptnr1_auth_seq_id / _pdbx_struct_conn_angle.ptnr1_label_asym_id / _pdbx_struct_conn_angle.ptnr1_label_atom_id / _pdbx_struct_conn_angle.ptnr1_label_comp_id / _pdbx_struct_conn_angle.ptnr1_label_seq_id / _pdbx_struct_conn_angle.ptnr3_auth_comp_id / _pdbx_struct_conn_angle.ptnr3_auth_seq_id / _pdbx_struct_conn_angle.ptnr3_label_asym_id / _pdbx_struct_conn_angle.ptnr3_label_atom_id / _pdbx_struct_conn_angle.ptnr3_label_comp_id / _pdbx_struct_conn_angle.ptnr3_label_seq_id / _pdbx_struct_conn_angle.value / _struct_conn.pdbx_dist_value / _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_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_conn.ptnr2_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: THYMIDINE KINASE, CYTOSOLIC
B: THYMIDINE KINASE, CYTOSOLIC
C: THYMIDINE KINASE, CYTOSOLIC
D: THYMIDINE KINASE, CYTOSOLIC
E: THYMIDINE KINASE, CYTOSOLIC
F: THYMIDINE KINASE, CYTOSOLIC
G: THYMIDINE KINASE, CYTOSOLIC
H: THYMIDINE KINASE, CYTOSOLIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)174,95727
Polymers170,5048
Non-polymers4,45419
Water19,3481074
1
A: THYMIDINE KINASE, CYTOSOLIC
B: THYMIDINE KINASE, CYTOSOLIC
C: THYMIDINE KINASE, CYTOSOLIC
D: THYMIDINE KINASE, CYTOSOLIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,46713
Polymers85,2524
Non-polymers2,2159
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area11990 Å2
ΔGint-61.97 kcal/mol
Surface area25830 Å2
MethodPISA
2
E: THYMIDINE KINASE, CYTOSOLIC
F: THYMIDINE KINASE, CYTOSOLIC
G: THYMIDINE KINASE, CYTOSOLIC
H: THYMIDINE KINASE, CYTOSOLIC
hetero molecules


Theoretical massNumber of molelcules
Total (without water)87,49114
Polymers85,2524
Non-polymers2,23910
Water724
TypeNameSymmetry operationNumber
identity operation1_555x,y,z1
Buried area12250 Å2
ΔGint-79.21 kcal/mol
Surface area26000 Å2
MethodPISA
Unit cell
Length a, b, c (Å)156.902, 123.252, 121.024
Angle α, β, γ (deg.)90.00, 132.98, 90.00
Int Tables number5
Space group name H-MC121

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Components

#1: Protein
THYMIDINE KINASE, CYTOSOLIC / / THYMIDINE KINASE 1


Mass: 21312.975 Da / Num. of mol.: 8 / Fragment: RESIDUES 1-193 / Mutation: YES
Source method: isolated from a genetically manipulated source
Details: TTP FEEDBACK INHIBITOR / Source: (gene. exp.) HOMO SAPIENS (human) / Plasmid: PGEX-2THUTK1-CDELTA41 / Production host: ESCHERICHIA COLI (E. coli) / Strain (production host): BL21 / References: UniProt: P04183, thymidine kinase
#2: Chemical
ChemComp-TTP / THYMIDINE-5'-TRIPHOSPHATE / Thymidine triphosphate


Mass: 482.168 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: C10H17N2O14P3
#3: Chemical
ChemComp-ZN / ZINC ION


Mass: 65.409 Da / Num. of mol.: 8 / Source method: obtained synthetically / Formula: Zn
#4: Chemical ChemComp-MG / MAGNESIUM ION


Mass: 24.305 Da / Num. of mol.: 3 / Source method: obtained synthetically / Formula: Mg
#5: Water ChemComp-HOH / water / Water


Mass: 18.015 Da / Num. of mol.: 1074 / Source method: isolated from a natural source / Formula: H2O
Compound detailsENGINEERED RESIDUE IN CHAIN A, THR 163 TO SER ENGINEERED RESIDUE IN CHAIN B, THR 163 TO SER ...ENGINEERED RESIDUE IN CHAIN A, THR 163 TO SER ENGINEERED RESIDUE IN CHAIN B, THR 163 TO SER ENGINEERED RESIDUE IN CHAIN C, THR 163 TO SER ENGINEERED RESIDUE IN CHAIN D, THR 163 TO SER ENGINEERED RESIDUE IN CHAIN E, THR 163 TO SER ENGINEERED RESIDUE IN CHAIN F, THR 163 TO SER ENGINEERED RESIDUE IN CHAIN G, THR 163 TO SER ENGINEERED RESIDUE IN CHAIN H, THR 163 TO SER
Nonpolymer detailsTHYMIDINE 5' TRIPHOSPHATE (TTP): TTP HAS TWO CONFORMATIONS IN EACH SITE. IN PROTEIN CHAINS A,B,C,E ...THYMIDINE 5' TRIPHOSPHATE (TTP): TTP HAS TWO CONFORMATIONS IN EACH SITE. IN PROTEIN CHAINS A,B,C,E AND F IS THE RATIO 1 TO 3 AND IN D, G AND H IS THE RATIO 3 TO 1 FOR RESPECTIVE CONFORMATION. MG HAS BEEN ASSIGNED FOR THE THE 3 TO 1 CONFORMATION.
Sequence detailsTRUNCATION AFTER AMINO ACID 193

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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: 2.7 Å3/Da / Density % sol: 43 % / Description: NONE
Crystal growMethod: vapor diffusion, hanging drop / pH: 5.6
Details: HANGING DROPS WITH EQUAL AMOUNTS OF PROTEIN, 10 MG PER ML CONTAINING 5 MM TTP AND TRAY SOLUTION COMPOSED OF SODIUM CITRATE PH 5.6, 2-PROPANOL AND PEG 4000.

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Data collection

DiffractionMean temperature: 100 K
Diffraction sourceSource: SYNCHROTRON / Site: ESRF / Beamline: ID23-2 / Wavelength: 0.8726
DetectorType: MARRESEARCH / Detector: CCD / Date: Apr 23, 2007
RadiationProtocol: SINGLE WAVELENGTH / Monochromatic (M) / Laue (L): M / Scattering type: x-ray
Radiation wavelengthWavelength: 0.8726 Å / Relative weight: 1
ReflectionResolution: 2.2→88.39 Å / Num. obs: 85203 / % possible obs: 99.9 % / Observed criterion σ(I): -3.7 / Redundancy: 3.7 % / Biso Wilson estimate: 24.5 Å2 / Rmerge(I) obs: 0.1 / Net I/σ(I): 10.56
Reflection shellResolution: 2.2→2.22 Å / Redundancy: 3.7 % / Rmerge(I) obs: 0.37 / Mean I/σ(I) obs: 3.4 / % possible all: 99.9

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Processing

Software
NameVersionClassification
REFMAC5.2.0019refinement
MOSFLMdata reduction
SCALAdata scaling
MOLREPphasing
RefinementMethod to determine structure: MOLECULAR REPLACEMENT
Starting model: PDB ENTRY 1XBT

1xbt


Resolution: 2.2→49.814 Å / Cor.coef. Fo:Fc: 0.947 / Cor.coef. Fo:Fc free: 0.917 / SU B: 4.75 / SU ML: 0.123 / Cross valid method: THROUGHOUT / ESU R: 0.218 / ESU R Free: 0.185 / Stereochemistry target values: MAXIMUM LIKELIHOOD
Details: HYDROGENS HAVE BEEN ADDED IN THE RIDING POSITIONS. LOOP CONTAINING RESIDUES 64 TO 73 IS MISSING IN THE STRUCTURE AS ARE RESIDUES BEFORE AMINO ACID 18 AND AFTER 192.
RfactorNum. reflection% reflectionSelection details
Rfree0.2209 4263 5.04 %RANDOM
Rwork0.1733 ---
obs0.176 85195 99.857 %-
Solvent computationIon probe radii: 0.8 Å / VDW probe radii: 1.2 Å / Solvent model: MASK BULK SOLVENT
Displacement parametersBiso mean: 21.101 Å2
Baniso -1Baniso -2Baniso -3
1--0.232 Å20 Å2-0.268 Å2
2---0.069 Å20 Å2
3----0.065 Å2
Refinement stepCycle: LAST / Resolution: 2.2→49.814 Å
ProteinNucleic acidLigandSolventTotal
Num. atoms9990 0 243 1074 11307
Refine LS restraints
Refine-IDTypeDev idealDev ideal targetNumber
X-RAY DIFFRACTIONr_bond_refined_d0.0080.02210377
X-RAY DIFFRACTIONr_bond_other_d
X-RAY DIFFRACTIONr_angle_refined_deg1.2152.00513999
X-RAY DIFFRACTIONr_angle_other_deg
X-RAY DIFFRACTIONr_dihedral_angle_1_deg5.91951274
X-RAY DIFFRACTIONr_dihedral_angle_2_deg33.46822.881420
X-RAY DIFFRACTIONr_dihedral_angle_3_deg15.446151856
X-RAY DIFFRACTIONr_dihedral_angle_4_deg20.351588
X-RAY DIFFRACTIONr_chiral_restr0.0850.21586
X-RAY DIFFRACTIONr_gen_planes_refined0.0030.027508
X-RAY DIFFRACTIONr_gen_planes_other
X-RAY DIFFRACTIONr_nbd_refined0.1820.24926
X-RAY DIFFRACTIONr_nbd_other
X-RAY DIFFRACTIONr_nbtor_refined0.3010.26930
X-RAY DIFFRACTIONr_nbtor_other
X-RAY DIFFRACTIONr_xyhbond_nbd_refined0.150.2896
X-RAY DIFFRACTIONr_xyhbond_nbd_other
X-RAY DIFFRACTIONr_metal_ion_refined0.0550.21
X-RAY DIFFRACTIONr_metal_ion_other
X-RAY DIFFRACTIONr_symmetry_vdw_refined0.2080.263
X-RAY DIFFRACTIONr_symmetry_vdw_other
X-RAY DIFFRACTIONr_symmetry_hbond_refined0.1270.230
X-RAY DIFFRACTIONr_symmetry_hbond_other
X-RAY DIFFRACTIONr_symmetry_metal_ion_refined
X-RAY DIFFRACTIONr_symmetry_metal_ion_other
X-RAY DIFFRACTIONr_mcbond_it0.4411.56576
X-RAY DIFFRACTIONr_mcbond_other
X-RAY DIFFRACTIONr_mcangle_it0.789210216
X-RAY DIFFRACTIONr_mcangle_other
X-RAY DIFFRACTIONr_scbond_it1.11534283
X-RAY DIFFRACTIONr_scbond_other
X-RAY DIFFRACTIONr_scangle_it1.8464.53783
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
LS refinement shellResolution: 2.2→2.257 Å / Total num. of bins used: 20
RfactorNum. reflection% reflection
Rfree0.293 360 -
Rwork0.209 5898 -
obs--99.809 %

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