data_2J4Q # _model_server_result.job_id 08xMokPs9J10bB99dvoDgA _model_server_result.datetime_utc '2024-11-16 04:59:28' _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 2j4q # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":194}' # _entry.id 2J4Q # _exptl.entry_id 2J4Q _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 402.188 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "THYMIDINE-5'-DIPHOSPHATE" _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 120 _cell.entry_id 2J4Q _cell.length_a 61.594 _cell.length_b 61.594 _cell.length_c 344.766 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2J4Q _symmetry.cell_setting ? _symmetry.Int_Tables_number 182 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63 2 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS trimeric 3 author_and_software_defined_assembly 1 PQS trimeric 3 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,F 1 1,2,3 B,D,E,G 2 1,4,5 # 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' 3_555 -x+y,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 0 0 0 3 'crystal symmetry operation' 2_555 -y,x-y,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 0 0 0 4 'crystal symmetry operation' 3_655 -x+y+1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 61.594 0 0 5 'crystal symmetry operation' 2_545 -y,x-y-1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 30.797 -53.341969 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # loop_ _struct_conn.conn_type_id _struct_conn.details _struct_conn.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.ptnr1_auth_asym_id _struct_conn.ptnr1_auth_comp_id _struct_conn.ptnr1_auth_seq_id _struct_conn.ptnr1_symmetry _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_conn.ptnr2_auth_asym_id _struct_conn.ptnr2_auth_comp_id _struct_conn.ptnr2_auth_seq_id _struct_conn.ptnr2_symmetry _struct_conn.pdbx_ptnr1_PDB_ins_code _struct_conn.pdbx_ptnr1_label_alt_id _struct_conn.pdbx_ptnr1_standard_comp_id _struct_conn.pdbx_ptnr2_PDB_ins_code _struct_conn.pdbx_ptnr2_label_alt_id _struct_conn.pdbx_ptnr3_PDB_ins_code _struct_conn.pdbx_ptnr3_label_alt_id _struct_conn.pdbx_ptnr3_label_asym_id _struct_conn.pdbx_ptnr3_label_atom_id _struct_conn.pdbx_ptnr3_label_comp_id _struct_conn.pdbx_ptnr3_label_seq_id _struct_conn.pdbx_PDB_id _struct_conn.pdbx_dist_value _struct_conn.pdbx_value_order metalc ? metalc1 D O2A TTP . B TTP 194 1_555 E MG MG . B MG 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? metalc ? metalc2 D O1G TTP . B TTP 194 1_555 E MG MG . B MG 195 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.504 ? # _chem_comp.formula 'C10 H16 N2 O11 P2' _chem_comp.formula_weight 402.188 _chem_comp.id TYD _chem_comp.mon_nstd_flag . _chem_comp.name "THYMIDINE-5'-DIPHOSPHATE" _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 PA O1A TYD doub 381 n n PA O2A TYD sing 382 n n PA O3A TYD sing 383 n n PA O5' TYD sing 384 n n O2A HOA2 TYD sing 385 n n O3A PB TYD sing 386 n n PB O1B TYD doub 387 n n PB O2B TYD sing 388 n n PB O3B TYD sing 389 n n O2B HOB2 TYD sing 390 n n O3B HOB3 TYD sing 391 n n O5' C5' TYD sing 392 n n C5' C4' TYD sing 393 n n C5' "H5'1" TYD sing 394 n n C5' "H5'2" TYD sing 395 n n C4' O4' TYD sing 396 n n C4' C3' TYD sing 397 n n C4' H4' TYD sing 398 n n O4' C1' TYD sing 399 n n C3' O3' TYD sing 400 n n C3' C2' TYD sing 401 n n C3' H3' TYD sing 402 n n O3' HO3' TYD sing 403 n n C2' C1' TYD sing 404 n n C2' "H2'1" TYD sing 405 n n C2' "H2'2" TYD sing 406 n n C1' N1 TYD sing 407 n n C1' H1' TYD sing 408 n n N1 C2 TYD sing 409 n y N1 C6 TYD sing 410 n y C2 O2 TYD doub 411 n n C2 N3 TYD sing 412 n y N3 C4 TYD sing 413 n y N3 HN3 TYD sing 414 n n C4 O4 TYD doub 415 n n C4 C5 TYD sing 416 n y C5 C5M TYD sing 417 n n C5 C6 TYD doub 418 n y C5M H51 TYD sing 419 n n C5M H52 TYD sing 420 n n C5M H53 TYD sing 421 n n C6 H6 TYD sing 422 n n # _atom_sites.entry_id 2J4Q _atom_sites.fract_transf_matrix[1][1] 0.016235 _atom_sites.fract_transf_matrix[1][2] 0.009373 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018747 _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] 0.002901 _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 C 2 TYD A 1 194 194 TYD TYD . D 3 TTP B 1 194 194 TTP TTP . E 4 MG B 1 195 195 MG MG . F 5 HOH A 1 2001 2001 HOH HOH . F 5 HOH A 2 2002 2002 HOH HOH . G 5 HOH B 1 2001 2001 HOH HOH . G 5 HOH B 2 2002 2002 HOH HOH . G 5 HOH B 3 2003 2003 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 PA TYD . . . C 2 10.735 -7.668 24.15 1 44.01 ? PA TYD 194 A 1 HETATM 2 O O1A TYD . . . C 2 10.893 -8.787 25.13 1 43.69 ? O1A TYD 194 A 1 HETATM 3 O O2A TYD . . . C 2 9.372 -7.119 23.834 1 40.8 ? O2A TYD 194 A 1 HETATM 4 O O3A TYD . . . C 2 11.378 -8.169 22.717 1 45.38 ? O3A TYD 194 A 1 HETATM 5 P PB TYD . . . C 2 12.324 -9.493 22.458 1 46.46 ? PB TYD 194 A 1 HETATM 6 O O1B TYD . . . C 2 11.736 -10.387 21.403 1 42.52 ? O1B TYD 194 A 1 HETATM 7 O O2B TYD . . . C 2 12.673 -10.096 23.788 1 47.25 ? O2B TYD 194 A 1 HETATM 8 O O3B TYD . . . C 2 13.678 -8.754 21.922 1 44.33 ? O3B TYD 194 A 1 HETATM 9 O O5' TYD . . . C 2 11.662 -6.433 24.671 1 42.3 ? O5' TYD 194 A 1 HETATM 10 C C5' TYD . . . C 2 13.002 -6.725 25.027 1 41.46 ? C5' TYD 194 A 1 HETATM 11 C C4' TYD . . . C 2 13.722 -5.614 25.472 1 43.59 ? C4' TYD 194 A 1 HETATM 12 O O4' TYD . . . C 2 14.065 -4.784 24.377 1 42.53 ? O4' TYD 194 A 1 HETATM 13 C C3' TYD . . . C 2 12.946 -4.829 26.358 1 43.84 ? C3' TYD 194 A 1 HETATM 14 O O3' TYD . . . C 2 13.452 -4.887 27.674 1 42.84 ? O3' TYD 194 A 1 HETATM 15 C C2' TYD . . . C 2 13.029 -3.504 25.962 1 43.08 ? C2' TYD 194 A 1 HETATM 16 C C1' TYD . . . C 2 13.734 -3.466 24.746 1 42.41 ? C1' TYD 194 A 1 HETATM 17 N N1 TYD . . . C 2 12.959 -2.757 23.881 1 42.44 ? N1 TYD 194 A 1 HETATM 18 C C2 TYD . . . C 2 13.541 -1.99 22.9 1 40.12 ? C2 TYD 194 A 1 HETATM 19 O O2 TYD . . . C 2 14.742 -1.963 22.721 1 40.78 ? O2 TYD 194 A 1 HETATM 20 N N3 TYD . . . C 2 12.778 -1.231 22.079 1 40.95 ? N3 TYD 194 A 1 HETATM 21 C C4 TYD . . . C 2 11.413 -1.184 22.196 1 41.84 ? C4 TYD 194 A 1 HETATM 22 O O4 TYD . . . C 2 10.803 -0.453 21.408 1 40.87 ? O4 TYD 194 A 1 HETATM 23 C C5 TYD . . . C 2 10.803 -1.937 23.21 1 42.02 ? C5 TYD 194 A 1 HETATM 24 C C5M TYD . . . C 2 9.33 -1.965 23.434 1 40.79 ? C5M TYD 194 A 1 HETATM 25 C C6 TYD . . . C 2 11.584 -2.727 24.041 1 42.89 ? C6 TYD 194 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 25 #