data_4LUJ # _model_server_result.job_id Pa71yIBSBDrw08IGdjRhag _model_server_result.datetime_utc '2024-11-05 00:31:01' _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 4luj # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":301}' # _entry.id 4LUJ # _exptl.entry_id 4LUJ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 340.181 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "6-HYDROXYURIDINE-5'-PHOSPHATE" _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 90.02 _cell.angle_gamma 90 _cell.entry_id 4LUJ _cell.length_a 47.811 _cell.length_b 47.567 _cell.length_c 85.714 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4LUJ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _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,E,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 ? 2 C N N ? 2 D N N # _chem_comp.formula 'C9 H13 N2 O10 P' _chem_comp.formula_weight 340.181 _chem_comp.id BMP _chem_comp.mon_nstd_flag . _chem_comp.name "6-HYDROXYURIDINE-5'-PHOSPHATE" _chem_comp.type 'rna linking' _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 OP1 BMP doub 70 n n P OP2 BMP sing 71 n n P OP3 BMP sing 72 n n P O5' BMP sing 73 n n OP2 HOP2 BMP sing 74 n n OP3 HOP3 BMP sing 75 n n O5' C5' BMP sing 76 n n C5' C4' BMP sing 77 n n C5' H5' BMP sing 78 n n C5' "H5''" BMP sing 79 n n C4' O4' BMP sing 80 n n C4' C3' BMP sing 81 n n C4' H4' BMP sing 82 n n O4' C1' BMP sing 83 n n C3' O3' BMP sing 84 n n C3' C2' BMP sing 85 n n C3' H3' BMP sing 86 n n O3' HO3' BMP sing 87 n n C2' O2' BMP sing 88 n n C2' C1' BMP sing 89 n n C2' H2' BMP sing 90 n n O2' HO2' BMP sing 91 n n C1' N1 BMP sing 92 n n C1' H1' BMP sing 93 n n N1 C2 BMP sing 94 n n N1 C6 BMP sing 95 n n C2 O2 BMP doub 96 n n C2 N3 BMP sing 97 n n N3 C4 BMP sing 98 n n N3 HN3 BMP sing 99 n n C4 O4 BMP doub 100 n n C4 C5 BMP sing 101 n n C5 C6 BMP doub 102 n n C5 H51 BMP sing 103 n n C6 O1 BMP sing 104 n n O1 HO1 BMP sing 105 n n # _atom_sites.entry_id 4LUJ _atom_sites.fract_transf_matrix[1][1] 0.020916 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000008 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021023 _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] 0.011667 _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 BMP A 1 301 239 BMP BMP . D 2 BMP B 1 301 239 BMP BMP . E 3 HOH A 1 401 1 HOH HOH . E 3 HOH A 2 402 3 HOH HOH . E 3 HOH A 3 403 4 HOH HOH . E 3 HOH A 4 404 8 HOH HOH . E 3 HOH A 5 405 11 HOH HOH . E 3 HOH A 6 406 12 HOH HOH . E 3 HOH A 7 407 13 HOH HOH . E 3 HOH A 8 408 18 HOH HOH . E 3 HOH A 9 409 19 HOH HOH . E 3 HOH A 10 410 24 HOH HOH . E 3 HOH A 11 411 25 HOH HOH . E 3 HOH A 12 412 26 HOH HOH . E 3 HOH A 13 413 27 HOH HOH . E 3 HOH A 14 414 28 HOH HOH . E 3 HOH A 15 415 32 HOH HOH . E 3 HOH A 16 416 35 HOH HOH . E 3 HOH A 17 417 36 HOH HOH . E 3 HOH A 18 418 37 HOH HOH . E 3 HOH A 19 419 39 HOH HOH . E 3 HOH A 20 420 41 HOH HOH . E 3 HOH A 21 421 42 HOH HOH . E 3 HOH A 22 422 44 HOH HOH . E 3 HOH A 23 423 45 HOH HOH . E 3 HOH A 24 424 46 HOH HOH . E 3 HOH A 25 425 49 HOH HOH . E 3 HOH A 26 426 50 HOH HOH . E 3 HOH A 27 427 52 HOH HOH . E 3 HOH A 28 428 54 HOH HOH . E 3 HOH A 29 429 56 HOH HOH . E 3 HOH A 30 430 57 HOH HOH . E 3 HOH A 31 431 61 HOH HOH . E 3 HOH A 32 432 67 HOH HOH . E 3 HOH A 33 433 68 HOH HOH . E 3 HOH A 34 434 70 HOH HOH . E 3 HOH A 35 435 72 HOH HOH . E 3 HOH A 36 436 73 HOH HOH . E 3 HOH A 37 437 77 HOH HOH . E 3 HOH A 38 438 78 HOH HOH . E 3 HOH A 39 439 83 HOH HOH . E 3 HOH A 40 440 86 HOH HOH . E 3 HOH A 41 441 89 HOH HOH . E 3 HOH A 42 442 90 HOH HOH . E 3 HOH A 43 443 91 HOH HOH . E 3 HOH A 44 444 95 HOH HOH . E 3 HOH A 45 445 96 HOH HOH . E 3 HOH A 46 446 97 HOH HOH . E 3 HOH A 47 447 99 HOH HOH . E 3 HOH A 48 448 100 HOH HOH . E 3 HOH A 49 449 101 HOH HOH . E 3 HOH A 50 450 104 HOH HOH . E 3 HOH A 51 451 105 HOH HOH . E 3 HOH A 52 452 106 HOH HOH . E 3 HOH A 53 453 108 HOH HOH . E 3 HOH A 54 454 109 HOH HOH . E 3 HOH A 55 455 110 HOH HOH . E 3 HOH A 56 456 111 HOH HOH . E 3 HOH A 57 457 113 HOH HOH . E 3 HOH A 58 458 114 HOH HOH . E 3 HOH A 59 459 115 HOH HOH . E 3 HOH A 60 460 118 HOH HOH . E 3 HOH A 61 461 120 HOH HOH . E 3 HOH A 62 462 122 HOH HOH . E 3 HOH A 63 463 123 HOH HOH . E 3 HOH A 64 464 124 HOH HOH . E 3 HOH A 65 465 126 HOH HOH . E 3 HOH A 66 466 127 HOH HOH . E 3 HOH A 67 467 128 HOH HOH . E 3 HOH A 68 468 129 HOH HOH . E 3 HOH A 69 469 131 HOH HOH . E 3 HOH A 70 470 135 HOH HOH . E 3 HOH A 71 471 137 HOH HOH . E 3 HOH A 72 472 139 HOH HOH . E 3 HOH A 73 473 141 HOH HOH . E 3 HOH A 74 474 145 HOH HOH . E 3 HOH A 75 475 146 HOH HOH . E 3 HOH A 76 476 147 HOH HOH . E 3 HOH A 77 477 150 HOH HOH . E 3 HOH A 78 478 151 HOH HOH . E 3 HOH A 79 479 152 HOH HOH . E 3 HOH A 80 480 153 HOH HOH . E 3 HOH A 81 481 154 HOH HOH . E 3 HOH A 82 482 155 HOH HOH . E 3 HOH A 83 483 157 HOH HOH . E 3 HOH A 84 484 159 HOH HOH . E 3 HOH A 85 485 161 HOH HOH . E 3 HOH A 86 486 163 HOH HOH . E 3 HOH A 87 487 165 HOH HOH . E 3 HOH A 88 488 167 HOH HOH . E 3 HOH A 89 489 169 HOH HOH . E 3 HOH A 90 490 174 HOH HOH . F 3 HOH B 1 401 2 HOH HOH . F 3 HOH B 2 402 5 HOH HOH . F 3 HOH B 3 403 6 HOH HOH . F 3 HOH B 4 404 7 HOH HOH . F 3 HOH B 5 405 9 HOH HOH . F 3 HOH B 6 406 10 HOH HOH . F 3 HOH B 7 407 14 HOH HOH . F 3 HOH B 8 408 15 HOH HOH . F 3 HOH B 9 409 16 HOH HOH . F 3 HOH B 10 410 17 HOH HOH . F 3 HOH B 11 411 20 HOH HOH . F 3 HOH B 12 412 21 HOH HOH . F 3 HOH B 13 413 22 HOH HOH . F 3 HOH B 14 414 23 HOH HOH . F 3 HOH B 15 415 29 HOH HOH . F 3 HOH B 16 416 30 HOH HOH . F 3 HOH B 17 417 31 HOH HOH . F 3 HOH B 18 418 33 HOH HOH . F 3 HOH B 19 419 34 HOH HOH . F 3 HOH B 20 420 38 HOH HOH . F 3 HOH B 21 421 40 HOH HOH . F 3 HOH B 22 422 43 HOH HOH . F 3 HOH B 23 423 47 HOH HOH . F 3 HOH B 24 424 48 HOH HOH . F 3 HOH B 25 425 51 HOH HOH . F 3 HOH B 26 426 53 HOH HOH . F 3 HOH B 27 427 55 HOH HOH . F 3 HOH B 28 428 58 HOH HOH . F 3 HOH B 29 429 59 HOH HOH . F 3 HOH B 30 430 60 HOH HOH . F 3 HOH B 31 431 62 HOH HOH . F 3 HOH B 32 432 63 HOH HOH . F 3 HOH B 33 433 64 HOH HOH . F 3 HOH B 34 434 65 HOH HOH . F 3 HOH B 35 435 66 HOH HOH . F 3 HOH B 36 436 69 HOH HOH . F 3 HOH B 37 437 71 HOH HOH . F 3 HOH B 38 438 74 HOH HOH . F 3 HOH B 39 439 75 HOH HOH . F 3 HOH B 40 440 76 HOH HOH . F 3 HOH B 41 441 79 HOH HOH . F 3 HOH B 42 442 80 HOH HOH . F 3 HOH B 43 443 81 HOH HOH . F 3 HOH B 44 444 82 HOH HOH . F 3 HOH B 45 445 84 HOH HOH . F 3 HOH B 46 446 85 HOH HOH . F 3 HOH B 47 447 87 HOH HOH . F 3 HOH B 48 448 88 HOH HOH . F 3 HOH B 49 449 92 HOH HOH . F 3 HOH B 50 450 93 HOH HOH . F 3 HOH B 51 451 94 HOH HOH . F 3 HOH B 52 452 98 HOH HOH . F 3 HOH B 53 453 102 HOH HOH . F 3 HOH B 54 454 103 HOH HOH . F 3 HOH B 55 455 107 HOH HOH . F 3 HOH B 56 456 112 HOH HOH . F 3 HOH B 57 457 116 HOH HOH . F 3 HOH B 58 458 117 HOH HOH . F 3 HOH B 59 459 119 HOH HOH . F 3 HOH B 60 460 121 HOH HOH . F 3 HOH B 61 461 125 HOH HOH . F 3 HOH B 62 462 130 HOH HOH . F 3 HOH B 63 463 132 HOH HOH . F 3 HOH B 64 464 133 HOH HOH . F 3 HOH B 65 465 134 HOH HOH . F 3 HOH B 66 466 136 HOH HOH . F 3 HOH B 67 467 138 HOH HOH . F 3 HOH B 68 468 140 HOH HOH . F 3 HOH B 69 469 142 HOH HOH . F 3 HOH B 70 470 143 HOH HOH . F 3 HOH B 71 471 144 HOH HOH . F 3 HOH B 72 472 148 HOH HOH . F 3 HOH B 73 473 149 HOH HOH . F 3 HOH B 74 474 156 HOH HOH . F 3 HOH B 75 475 158 HOH HOH . F 3 HOH B 76 476 160 HOH HOH . F 3 HOH B 77 477 162 HOH HOH . F 3 HOH B 78 478 164 HOH HOH . F 3 HOH B 79 479 166 HOH HOH . F 3 HOH B 80 480 168 HOH HOH . F 3 HOH B 81 481 170 HOH HOH . F 3 HOH B 82 482 172 HOH HOH . F 3 HOH B 83 483 173 HOH HOH . F 3 HOH B 84 484 175 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 BMP . . . D 2 -36.777 -9.382 4.389 1 27.99 ? P BMP 301 B 1 HETATM 2 O OP1 BMP . . . D 2 -38.065 -10.118 4.445 1 30.89 ? OP1 BMP 301 B 1 HETATM 3 O OP2 BMP . . . D 2 -35.453 -10.206 4.058 1 30.64 ? OP2 BMP 301 B 1 HETATM 4 O OP3 BMP . . . D 2 -36.898 -8.137 3.385 1 27.68 ? OP3 BMP 301 B 1 HETATM 5 O O5' BMP . . . D 2 -36.459 -8.782 5.83 1 28.18 ? O5' BMP 301 B 1 HETATM 6 C C5' BMP . . . D 2 -37.491 -8.332 6.697 1 27.7 ? C5' BMP 301 B 1 HETATM 7 C C4' BMP . . . D 2 -36.907 -7.963 8.032 1 25.78 ? C4' BMP 301 B 1 HETATM 8 O O4' BMP . . . D 2 -37.929 -7.36 8.871 1 25.37 ? O4' BMP 301 B 1 HETATM 9 C C3' BMP . . . D 2 -36.354 -9.145 8.821 1 24.12 ? C3' BMP 301 B 1 HETATM 10 O O3' BMP . . . D 2 -35.256 -8.703 9.616 1 25.25 ? O3' BMP 301 B 1 HETATM 11 C C2' BMP . . . D 2 -37.52 -9.525 9.726 1 24.85 ? C2' BMP 301 B 1 HETATM 12 O O2' BMP . . . D 2 -37.13 -10.196 10.913 1 26.58 ? O2' BMP 301 B 1 HETATM 13 C C1' BMP . . . D 2 -38.15 -8.161 10.022 1 23.87 ? C1' BMP 301 B 1 HETATM 14 N N1 BMP . . . D 2 -39.605 -8.183 10.247 1 23.1 ? N1 BMP 301 B 1 HETATM 15 C C2 BMP . . . D 2 -40.469 -8.726 9.359 1 24.92 ? C2 BMP 301 B 1 HETATM 16 O O2 BMP . . . D 2 -40.103 -9.28 8.331 1 26.19 ? O2 BMP 301 B 1 HETATM 17 N N3 BMP . . . D 2 -41.789 -8.686 9.587 1 25.43 ? N3 BMP 301 B 1 HETATM 18 C C4 BMP . . . D 2 -42.3 -8.093 10.68 1 25.59 ? C4 BMP 301 B 1 HETATM 19 O O4 BMP . . . D 2 -43.507 -8.068 10.828 1 26.36 ? O4 BMP 301 B 1 HETATM 20 C C5 BMP . . . D 2 -41.438 -7.503 11.62 1 23.65 ? C5 BMP 301 B 1 HETATM 21 C C6 BMP . . . D 2 -40.093 -7.549 11.372 1 24.48 ? C6 BMP 301 B 1 HETATM 22 O O1 BMP . . . D 2 -39.228 -6.973 12.217 1 26.85 ? O1 BMP 301 B 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 272 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #