data_2VTK # _model_server_result.job_id 9Lee9mthZh3McLy_hJB8yg _model_server_result.datetime_utc '2024-10-16 10:25:46' _model_server_result.server_version 0.9.12 _model_server_result.query_name ligand _model_server_result.source_id pdb-bcif _model_server_result.entry_id 2vtk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 2VTK # _exptl.entry_id 2VTK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 242.229 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description THYMIDINE _entity.pdbx_number_of_molecules 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 2VTK _cell.length_a 84.1 _cell.length_b 84.1 _cell.length_c 155.36 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2VTK _symmetry.cell_setting ? _symmetry.Int_Tables_number 80 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'I 41' # _pdbx_struct_assembly.method_details PISA,PQS _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 6_655 -x+1,-y,z -1 0 0 0 -1 0 0 0 1 84.1 0 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C10 H14 N2 O5' _chem_comp.formula_weight 242.229 _chem_comp.id THM _chem_comp.mon_nstd_flag . _chem_comp.name THYMIDINE _chem_comp.type 'dna oh 5 prime terminus' _chem_comp.pdbx_synonyms "DEOXYTHYMIDINE;2'-DEOXYTHYMIDINE" # loop_ _chem_comp_bond.atom_id_1 _chem_comp_bond.atom_id_2 _chem_comp_bond.comp_id _chem_comp_bond.value_order _chem_comp_bond.pdbx_ordinal _chem_comp_bond.pdbx_stereo_config _chem_comp_bond.pdbx_aromatic_flag O5' C5' THM sing 334 n n O5' HO5' THM sing 335 n n C5' C4' THM sing 336 n n C5' "H5'1" THM sing 337 n n C5' "H5'2" THM sing 338 n n C4' O4' THM sing 339 n n C4' C3' THM sing 340 n n C4' H4' THM sing 341 n n O4' C1' THM sing 342 n n C3' O3' THM sing 343 n n C3' C2' THM sing 344 n n C3' H3' THM sing 345 n n O3' HO3' THM sing 346 n n C2' C1' THM sing 347 n n C2' "H2'1" THM sing 348 n n C2' "H2'2" THM sing 349 n n C1' N1 THM sing 350 n n C1' H1' THM sing 351 n n N1 C2 THM sing 352 n n N1 C6 THM sing 353 n n C2 O2 THM doub 354 n n C2 N3 THM sing 355 n n N3 C4 THM sing 356 n n N3 HN3 THM sing 357 n n C4 O4 THM doub 358 n n C4 C5 THM sing 359 n n C5 C5M THM sing 360 n n C5 C6 THM doub 361 n n C5M HM51 THM sing 362 n n C5M HM52 THM sing 363 n n C5M HM53 THM sing 364 n n C6 H6 THM sing 365 n n # _atom_sites.entry_id 2VTK _atom_sites.fract_transf_matrix[1][1] 0.011891 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011891 _atom_sites.fract_transf_matrix[2][3] 0 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.006437 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # loop_ _pdbx_nonpoly_scheme.asym_id _pdbx_nonpoly_scheme.entity_id _pdbx_nonpoly_scheme.mon_id _pdbx_nonpoly_scheme.pdb_strand_id _pdbx_nonpoly_scheme.ndb_seq_num _pdbx_nonpoly_scheme.pdb_seq_num _pdbx_nonpoly_scheme.auth_seq_num _pdbx_nonpoly_scheme.pdb_mon_id _pdbx_nonpoly_scheme.auth_mon_id _pdbx_nonpoly_scheme.pdb_ins_code B 2 ADP A 1 400 400 ADP ADP . C 3 THM A 1 500 500 THM THM . D 4 HOH A 1 601 601 HOH HOH . D 4 HOH A 2 602 602 HOH HOH . D 4 HOH A 3 603 603 HOH HOH . D 4 HOH A 4 604 604 HOH HOH . D 4 HOH A 5 605 605 HOH HOH . D 4 HOH A 6 606 606 HOH HOH . D 4 HOH A 7 607 607 HOH HOH . D 4 HOH A 8 608 608 HOH HOH . D 4 HOH A 9 609 609 HOH HOH . D 4 HOH A 10 610 610 HOH HOH . D 4 HOH A 11 611 611 HOH HOH . D 4 HOH A 12 612 612 HOH HOH . D 4 HOH A 13 613 613 HOH HOH . D 4 HOH A 14 614 614 HOH HOH . D 4 HOH A 15 615 615 HOH HOH . D 4 HOH A 16 616 616 HOH HOH . D 4 HOH A 17 617 617 HOH HOH . D 4 HOH A 18 618 618 HOH HOH . D 4 HOH A 19 619 619 HOH HOH . D 4 HOH A 20 620 620 HOH HOH . D 4 HOH A 21 621 621 HOH HOH . D 4 HOH A 22 622 622 HOH HOH . D 4 HOH A 23 623 623 HOH HOH . D 4 HOH A 24 624 624 HOH HOH . D 4 HOH A 25 625 625 HOH HOH . D 4 HOH A 26 626 626 HOH HOH . D 4 HOH A 27 627 627 HOH HOH . D 4 HOH A 28 628 628 HOH HOH . # loop_ _atom_site.group_PDB _atom_site.id _atom_site.type_symbol _atom_site.label_atom_id _atom_site.label_comp_id _atom_site.label_seq_id _atom_site.label_alt_id _atom_site.pdbx_PDB_ins_code _atom_site.label_asym_id _atom_site.label_entity_id _atom_site.Cartn_x _atom_site.Cartn_y _atom_site.Cartn_z _atom_site.occupancy _atom_site.B_iso_or_equiv _atom_site.pdbx_formal_charge _atom_site.auth_atom_id _atom_site.auth_comp_id _atom_site.auth_seq_id _atom_site.auth_asym_id _atom_site.pdbx_PDB_model_num HETATM 1 O O5' THM . . . C 3 41.351 19.492 32.62 1 39.34 ? O5' THM 500 A 1 HETATM 2 C C5' THM . . . C 3 41.196 18.088 32.444 1 22.49 ? C5' THM 500 A 1 HETATM 3 C C4' THM . . . C 3 40.955 17.872 30.999 1 17.26 ? C4' THM 500 A 1 HETATM 4 O O4' THM . . . C 3 41.02 16.479 30.739 1 18.51 ? O4' THM 500 A 1 HETATM 5 C C3' THM . . . C 3 39.617 18.313 30.526 1 12.71 ? C3' THM 500 A 1 HETATM 6 O O3' THM . . . C 3 39.686 18.555 29.119 1 16.42 ? O3' THM 500 A 1 HETATM 7 C C2' THM . . . C 3 38.759 17.148 30.908 1 10.86 ? C2' THM 500 A 1 HETATM 8 C C1' THM . . . C 3 39.675 15.987 30.541 1 18.31 ? C1' THM 500 A 1 HETATM 9 N N1 THM . . . C 3 39.596 14.835 31.447 1 19.71 ? N1 THM 500 A 1 HETATM 10 C C2 THM . . . C 3 39.243 13.637 30.922 1 21.76 ? C2 THM 500 A 1 HETATM 11 O O2 THM . . . C 3 38.941 13.523 29.737 1 23.36 ? O2 THM 500 A 1 HETATM 12 N N3 THM . . . C 3 39.227 12.549 31.752 1 26.99 ? N3 THM 500 A 1 HETATM 13 C C4 THM . . . C 3 39.56 12.636 33.088 1 30.81 ? C4 THM 500 A 1 HETATM 14 O O4 THM . . . C 3 39.521 11.621 33.788 1 26.96 ? O4 THM 500 A 1 HETATM 15 C C5 THM . . . C 3 39.932 13.882 33.602 1 27.32 ? C5 THM 500 A 1 HETATM 16 C C5M THM . . . C 3 40.301 13.995 35.033 1 28.6 ? C5M THM 500 A 1 HETATM 17 C C6 THM . . . C 3 39.948 14.983 32.752 1 25.19 ? C6 THM 500 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 255 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 17 #