data_5W0O # _model_server_result.job_id 2xCRh3WX4fO6sTDKhGB0Pg _model_server_result.datetime_utc '2024-11-04 22:47:52' _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 5w0o # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":1401}' # _entry.id 5W0O # _exptl.entry_id 5W0O _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 484.141 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE 5'-TRIPHOSPHATE" _entity.pdbx_number_of_molecules 2 _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 5W0O _cell.length_a 66.825 _cell.length_b 80.851 _cell.length_c 181.83 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5W0O _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA trimeric 3 author_and_software_defined_assembly 1 PISA 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,D,E,G,I,J 1 1 B,C,D,F,H,I,J 2 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 E N N ? 3 F N 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 hydrog WATSON-CRICK hydrog1 C N1 G 1 C G 1 1_555 D N3 C 14 D C 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 C N2 G 1 C G 1 1_555 D O2 C 14 D C 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 C O6 G 1 C G 1 1_555 D N4 C 14 D C 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 C N3 C 2 C C 2 1_555 D N1 G 13 D G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 C N4 C 2 C C 2 1_555 D O6 G 13 D G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 C O2 C 2 C C 2 1_555 D N2 G 13 D G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 C N1 G 3 C G 3 1_555 D N3 C 12 D C 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 C N2 G 3 C G 3 1_555 D O2 C 12 D C 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 C O6 G 3 C G 3 1_555 D N4 C 12 D C 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 C N1 A 4 C A 4 1_555 D N3 U 11 D U 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 C N6 A 4 C A 4 1_555 D O4 U 11 D U 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 C N1 A 5 C A 5 1_555 D N3 U 10 D U 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 C N6 A 5 C A 5 1_555 D O4 U 10 D U 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 C N1 G 6 C G 6 1_555 D N3 C 9 D C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 C N2 G 6 C G 6 1_555 D O2 C 9 D C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 C O6 G 6 C G 6 1_555 D N4 C 9 D C 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 C N3 C 7 C C 7 1_555 D N1 G 8 D G 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 C N4 C 7 C C 7 1_555 D O6 G 8 D G 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog19 C O2 C 7 C C 7 1_555 D N2 G 8 D G 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog20 C N1 G 8 C G 8 1_555 D N3 C 7 D C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog21 C N2 G 8 C G 8 1_555 D O2 C 7 D C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog22 C O6 G 8 C G 8 1_555 D N4 C 7 D C 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog23 C N3 C 9 C C 9 1_555 D N1 G 6 D G 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog24 C N4 C 9 C C 9 1_555 D O6 G 6 D G 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog25 C O2 C 9 C C 9 1_555 D N2 G 6 D G 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog26 C N3 U 10 C U 10 1_555 D N1 A 5 D A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog27 C O4 U 10 C U 10 1_555 D N6 A 5 D A 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog28 C N3 U 11 C U 11 1_555 D N1 A 4 D A 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog29 C O4 U 11 C U 11 1_555 D N6 A 4 D A 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog30 C N3 C 12 C C 12 1_555 D N1 G 3 D G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog31 C N4 C 12 C C 12 1_555 D O6 G 3 D G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog32 C O2 C 12 C C 12 1_555 D N2 G 3 D G 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog33 C N1 G 13 C G 13 1_555 D N3 C 2 D C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog34 C N2 G 13 C G 13 1_555 D O2 C 2 D C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog35 C O6 G 13 C G 13 1_555 D N4 C 2 D C 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog36 C N3 C 14 C C 14 1_555 D N1 G 1 D G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog37 C N4 C 14 C C 14 1_555 D O6 G 1 D G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog38 C O2 C 14 C C 14 1_555 D N2 G 1 D G 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C9 H15 N2 O15 P3' _chem_comp.formula_weight 484.141 _chem_comp.id UTP _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE 5'-TRIPHOSPHATE" _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 UTP doub 508 n n PA O2A UTP sing 509 n n PA O3A UTP sing 510 n n PA O5' UTP sing 511 n n O2A H2A UTP sing 512 n n O3A PB UTP sing 513 n n O5' C5' UTP sing 514 n n PB O1B UTP sing 515 n n PB O2B UTP doub 516 n n PB O3B UTP sing 517 n n O1B H1B UTP sing 518 n n O3B PG UTP sing 519 n n PG O1G UTP sing 520 n n PG O2G UTP doub 521 n n PG O3G UTP sing 522 n n O1G H1G UTP sing 523 n n O3G H3G UTP sing 524 n n C5' C4' UTP sing 525 n n C5' "H5'1" UTP sing 526 n n C5' "H5'2" UTP sing 527 n n C4' O4' UTP sing 528 n n C4' C3' UTP sing 529 n n C4' H4' UTP sing 530 n n O4' C1' UTP sing 531 n n C1' C2' UTP sing 532 n n C1' N1 UTP sing 533 n n C1' H1' UTP sing 534 n n C2' O2' UTP sing 535 n n C2' C3' UTP sing 536 n n C2' H2' UTP sing 537 n n O2' HA UTP sing 538 n n C3' O3' UTP sing 539 n n C3' H3' UTP sing 540 n n O3' HB UTP sing 541 n n N1 C6 UTP sing 542 n y N1 C2 UTP sing 543 n y C6 C5 UTP doub 544 n y C6 H6 UTP sing 545 n n C2 O2 UTP doub 546 n n C2 N3 UTP sing 547 n y N3 C4 UTP sing 548 n y N3 H3 UTP sing 549 n n C4 O4 UTP doub 550 n n C4 C5 UTP sing 551 n y C5 H5 UTP sing 552 n n # _atom_sites.entry_id 5W0O _atom_sites.fract_transf_matrix[1][1] 0.014964 _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] 0.012368 _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] 0.0055 _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 E 3 UTP A 1 1401 902 UTP UTP . F 3 UTP B 1 1401 901 UTP UTP . G 4 HOH A 1 1501 1 HOH HOH . G 4 HOH A 2 1502 34 HOH HOH . G 4 HOH A 3 1503 12 HOH HOH . G 4 HOH A 4 1504 16 HOH HOH . G 4 HOH A 5 1505 20 HOH HOH . G 4 HOH A 6 1506 40 HOH HOH . G 4 HOH A 7 1507 6 HOH HOH . G 4 HOH A 8 1508 4 HOH HOH . G 4 HOH A 9 1509 31 HOH HOH . G 4 HOH A 10 1510 24 HOH HOH . G 4 HOH A 11 1511 35 HOH HOH . G 4 HOH A 12 1512 27 HOH HOH . G 4 HOH A 13 1513 19 HOH HOH . G 4 HOH A 14 1514 7 HOH HOH . G 4 HOH A 15 1515 9 HOH HOH . G 4 HOH A 16 1516 45 HOH HOH . G 4 HOH A 17 1517 26 HOH HOH . G 4 HOH A 18 1518 30 HOH HOH . G 4 HOH A 19 1519 21 HOH HOH . G 4 HOH A 20 1520 48 HOH HOH . G 4 HOH A 21 1521 29 HOH HOH . G 4 HOH A 22 1522 50 HOH HOH . G 4 HOH A 23 1523 18 HOH HOH . G 4 HOH A 24 1524 11 HOH HOH . G 4 HOH A 25 1525 23 HOH HOH . G 4 HOH A 26 1526 44 HOH HOH . G 4 HOH A 27 1527 17 HOH HOH . G 4 HOH A 28 1528 2 HOH HOH . H 4 HOH B 1 1501 39 HOH HOH . H 4 HOH B 2 1502 25 HOH HOH . H 4 HOH B 3 1503 13 HOH HOH . H 4 HOH B 4 1504 32 HOH HOH . H 4 HOH B 5 1505 46 HOH HOH . H 4 HOH B 6 1506 5 HOH HOH . H 4 HOH B 7 1507 8 HOH HOH . H 4 HOH B 8 1508 37 HOH HOH . H 4 HOH B 9 1509 15 HOH HOH . H 4 HOH B 10 1510 22 HOH HOH . H 4 HOH B 11 1511 14 HOH HOH . H 4 HOH B 12 1512 38 HOH HOH . H 4 HOH B 13 1513 41 HOH HOH . H 4 HOH B 14 1514 49 HOH HOH . H 4 HOH B 15 1515 28 HOH HOH . H 4 HOH B 16 1516 42 HOH HOH . I 4 HOH C 1 101 3 HOH HOH . I 4 HOH C 2 102 43 HOH HOH . I 4 HOH C 3 103 10 HOH HOH . I 4 HOH C 4 104 33 HOH HOH . I 4 HOH C 5 105 36 HOH HOH . J 4 HOH D 1 101 47 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 UTP . . . E 3 -38.97 89.12 11.881 1 55.83 ? PA UTP 1401 A 1 HETATM 2 O O1A UTP . . . E 3 -38.975 90.622 11.968 1 53.57 ? O1A UTP 1401 A 1 HETATM 3 O O2A UTP . . . E 3 -38.181 88.23 12.823 1 62 ? O2A UTP 1401 A 1 HETATM 4 O O3A UTP . . . E 3 -40.48 88.57 11.979 1 53.97 ? O3A UTP 1401 A 1 HETATM 5 O O5' UTP . . . E 3 -38.565 88.676 10.397 1 55.56 ? O5' UTP 1401 A 1 HETATM 6 P PB UTP . . . E 3 -41.801 89.479 11.808 1 48.41 ? PB UTP 1401 A 1 HETATM 7 O O1B UTP . . . E 3 -41.9 90.538 12.897 1 55.09 ? O1B UTP 1401 A 1 HETATM 8 O O2B UTP . . . E 3 -41.946 89.849 10.343 1 47.74 ? O2B UTP 1401 A 1 HETATM 9 O O3B UTP . . . E 3 -42.882 88.347 12.211 1 70.73 ? O3B UTP 1401 A 1 HETATM 10 P PG UTP . . . E 3 -43.397 87.166 11.238 1 64.1 ? PG UTP 1401 A 1 HETATM 11 O O1G UTP . . . E 3 -44.611 87.779 10.588 1 67.12 ? O1G UTP 1401 A 1 HETATM 12 O O2G UTP . . . E 3 -42.238 86.889 10.317 1 66.71 ? O2G UTP 1401 A 1 HETATM 13 O O3G UTP . . . E 3 -43.735 86.023 12.171 1 57.86 ? O3G UTP 1401 A 1 HETATM 14 C C5' UTP . . . E 3 -38.796 89.544 9.294 1 52.03 ? C5' UTP 1401 A 1 HETATM 15 C C4' UTP . . . E 3 -38.811 88.675 8.05 1 51.91 ? C4' UTP 1401 A 1 HETATM 16 O O4' UTP . . . E 3 -37.484 88.227 7.763 1 55.64 ? O4' UTP 1401 A 1 HETATM 17 C C1' UTP . . . E 3 -37.516 86.915 7.201 1 53.48 ? C1' UTP 1401 A 1 HETATM 18 C C2' UTP . . . E 3 -38.967 86.464 7.237 1 54.58 ? C2' UTP 1401 A 1 HETATM 19 O O2' UTP . . . E 3 -39.55 86.704 5.956 1 57.22 ? O2' UTP 1401 A 1 HETATM 20 C C3' UTP . . . E 3 -39.61 87.395 8.241 1 52.38 ? C3' UTP 1401 A 1 HETATM 21 O O3' UTP . . . E 3 -40.994 87.579 7.961 1 53.67 ? O3' UTP 1401 A 1 HETATM 22 N N1 UTP . . . E 3 -36.757 85.966 8.019 1 48.65 ? N1 UTP 1401 A 1 HETATM 23 C C6 UTP . . . E 3 -36.529 86.2 9.317 1 47.68 ? C6 UTP 1401 A 1 HETATM 24 C C2 UTP . . . E 3 -36.312 84.765 7.432 1 49.27 ? C2 UTP 1401 A 1 HETATM 25 O O2 UTP . . . E 3 -36.536 84.552 6.224 1 53.19 ? O2 UTP 1401 A 1 HETATM 26 N N3 UTP . . . E 3 -35.639 83.869 8.149 1 47.43 ? N3 UTP 1401 A 1 HETATM 27 C C4 UTP . . . E 3 -35.394 84.088 9.446 1 47.2 ? C4 UTP 1401 A 1 HETATM 28 O O4 UTP . . . E 3 -34.772 83.227 10.107 1 51.93 ? O4 UTP 1401 A 1 HETATM 29 C C5 UTP . . . E 3 -35.835 85.253 10.063 1 46.57 ? C5 UTP 1401 A 1 # _model_server_stats.io_time_ms 124 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 273 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 29 #