data_1VTK # _model_server_result.job_id uWLCWHknOu8sUkghrnLQLQ _model_server_result.datetime_utc '2024-11-23 12:40:12' _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 1vtk # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":500}' # _entry.id 1VTK # _exptl.entry_id 1VTK _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 322.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-PHOSPHATE" _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 1VTK _cell.length_a 83.4 _cell.length_b 83.4 _cell.length_c 156.7 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1VTK _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 83.4 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 H15 N2 O8 P' _chem_comp.formula_weight 322.208 _chem_comp.id TMP _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # 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 P O1P TMP doub 350 n n P O2P TMP sing 351 n n P O3P TMP sing 352 n n P O5' TMP sing 353 n n O2P HOP2 TMP sing 354 n n O3P HOP3 TMP sing 355 n n O5' C5' TMP sing 356 n n C5' C4' TMP sing 357 n n C5' "H5'1" TMP sing 358 n n C5' "H5'2" TMP sing 359 n n C4' O4' TMP sing 360 n n C4' C3' TMP sing 361 n n C4' H4' TMP sing 362 n n O4' C1' TMP sing 363 n n C3' O3' TMP sing 364 n n C3' C2' TMP sing 365 n n C3' H3' TMP sing 366 n n O3' HO3' TMP sing 367 n n C2' C1' TMP sing 368 n n C2' "H2'1" TMP sing 369 n n C2' "H2'2" TMP sing 370 n n C1' N1 TMP sing 371 n n C1' H1' TMP sing 372 n n N1 C2 TMP sing 373 n n N1 C6 TMP sing 374 n n C2 O2 TMP doub 375 n n C2 N3 TMP sing 376 n n N3 C4 TMP sing 377 n n N3 HN3 TMP sing 378 n n C4 O4 TMP doub 379 n n C4 C5 TMP sing 380 n n C5 C5M TMP sing 381 n n C5 C6 TMP doub 382 n n C5M H51 TMP sing 383 n n C5M H52 TMP sing 384 n n C5M H53 TMP sing 385 n n C6 H6 TMP sing 386 n n # _atom_sites.entry_id 1VTK _atom_sites.fract_transf_matrix[1][1] 0.01199 _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] 0.01199 _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] 0.006382 _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 TMP A 1 500 500 TMP TMP . 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 . D 4 HOH A 29 629 629 HOH HOH . D 4 HOH A 30 630 630 HOH HOH . D 4 HOH A 31 631 631 HOH HOH . D 4 HOH A 32 632 632 HOH HOH . D 4 HOH A 33 633 633 HOH HOH . D 4 HOH A 34 634 634 HOH HOH . D 4 HOH A 35 635 635 HOH HOH . D 4 HOH A 36 636 636 HOH HOH . D 4 HOH A 37 637 637 HOH HOH . D 4 HOH A 38 638 638 HOH HOH . D 4 HOH A 39 639 639 HOH HOH . D 4 HOH A 40 640 640 HOH HOH . D 4 HOH A 41 641 641 HOH HOH . D 4 HOH A 42 642 642 HOH HOH . D 4 HOH A 43 643 643 HOH HOH . D 4 HOH A 44 644 644 HOH HOH . D 4 HOH A 45 645 645 HOH HOH . D 4 HOH A 46 646 646 HOH HOH . D 4 HOH A 47 647 647 HOH HOH . D 4 HOH A 48 648 648 HOH HOH . D 4 HOH A 49 649 649 HOH HOH . D 4 HOH A 50 650 650 HOH HOH . D 4 HOH A 51 651 651 HOH HOH . D 4 HOH A 52 652 652 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 P P TMP . . . C 3 39.914 20.657 33.304 1 37.52 ? P TMP 500 A 1 HETATM 2 O O1P TMP . . . C 3 38.994 20.458 34.43 1 39.12 ? O1P TMP 500 A 1 HETATM 3 O O2P TMP . . . C 3 39.391 21.72 32.418 1 38.41 ? O2P TMP 500 A 1 HETATM 4 O O3P TMP . . . C 3 41.261 20.994 33.795 1 28.61 ? O3P TMP 500 A 1 HETATM 5 O O5' TMP . . . C 3 39.996 19.281 32.47 1 33.74 ? O5' TMP 500 A 1 HETATM 6 C C5' TMP . . . C 3 41.022 19.021 31.503 1 26.1 ? C5' TMP 500 A 1 HETATM 7 C C4' TMP . . . C 3 40.415 18.203 30.408 1 15.9 ? C4' TMP 500 A 1 HETATM 8 O O4' TMP . . . C 3 40.505 16.827 30.759 1 13.03 ? O4' TMP 500 A 1 HETATM 9 C C3' TMP . . . C 3 38.968 18.502 30.148 1 18.39 ? C3' TMP 500 A 1 HETATM 10 O O3' TMP . . . C 3 38.768 18.664 28.742 1 25.79 ? O3' TMP 500 A 1 HETATM 11 C C2' TMP . . . C 3 38.262 17.307 30.751 1 11.56 ? C2' TMP 500 A 1 HETATM 12 C C1' TMP . . . C 3 39.258 16.216 30.469 1 14.29 ? C1' TMP 500 A 1 HETATM 13 N N1 TMP . . . C 3 39.199 15.057 31.39 1 18.58 ? N1 TMP 500 A 1 HETATM 14 C C2 TMP . . . C 3 38.849 13.851 30.873 1 20.27 ? C2 TMP 500 A 1 HETATM 15 O O2 TMP . . . C 3 38.532 13.725 29.687 1 22.16 ? O2 TMP 500 A 1 HETATM 16 N N3 TMP . . . C 3 38.847 12.763 31.707 1 25.52 ? N3 TMP 500 A 1 HETATM 17 C C4 TMP . . . C 3 39.185 12.839 33.029 1 23.6 ? C4 TMP 500 A 1 HETATM 18 O O4 TMP . . . C 3 39.153 11.817 33.712 1 21.3 ? O4 TMP 500 A 1 HETATM 19 C C5 TMP . . . C 3 39.549 14.079 33.55 1 20.22 ? C5 TMP 500 A 1 HETATM 20 C C5M TMP . . . C 3 39.914 14.175 34.986 1 15.96 ? C5M TMP 500 A 1 HETATM 21 C C6 TMP . . . C 3 39.559 15.199 32.699 1 22.38 ? C6 TMP 500 A 1 # _model_server_stats.io_time_ms 69 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 241 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 21 #