data_6QXH # _model_server_result.job_id A8uvqEFLTX3INasc8J-o6A _model_server_result.datetime_utc '2024-11-27 06:19:08' _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 6qxh # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":401}' # _entry.id 6QXH # _exptl.entry_id 6QXH _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 308.182 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _entity.pdbx_number_of_molecules 3 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 115.38 _cell.angle_gamma 90 _cell.entry_id 6QXH _cell.length_a 182.11 _cell.length_b 61.59 _cell.length_c 101.1 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6QXH _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # 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 dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 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,B,D,E,F,G,J,K 1 1 C,H,I,L 2 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' 2_455 -x-1,y,-z -1 0 0 0 1 0 0 0 -1 -182.11 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 D N N ? 2 G N N ? 2 H 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 covale ? covale1 A C ARG 54 A ARG 42 1_555 A N SCH 55 A SCH 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? covale ? covale2 A C SCH 55 A SCH 43 1_555 A N GLY 56 A GLY 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.336 ? covale ? covale3 B C ARG 54 B ARG 42 1_555 B N SCH 55 B SCH 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.34 ? covale ? covale4 B C SCH 55 B SCH 43 1_555 B N GLY 56 B GLY 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.322 ? covale ? covale5 C C ARG 54 C ARG 42 1_555 C N SCH 55 C SCH 43 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale6 C C SCH 55 C SCH 43 1_555 C N GLY 56 C GLY 44 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.342 ? # _chem_comp.formula 'C9 H13 N2 O8 P' _chem_comp.formula_weight 308.182 _chem_comp.id UMP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-MONOPHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms DUMP # 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 N1 C2 UMP sing 395 n n N1 C6 UMP sing 396 n n N1 C1' UMP sing 397 n n C2 N3 UMP sing 398 n n C2 O2 UMP doub 399 n n N3 C4 UMP sing 400 n n N3 HN3 UMP sing 401 n n C4 C5 UMP sing 402 n n C4 O4 UMP doub 403 n n C5 C6 UMP doub 404 n n C5 H5 UMP sing 405 n n C6 H6 UMP sing 406 n n C1' C2' UMP sing 407 n n C1' O4' UMP sing 408 n n C1' H1' UMP sing 409 n n C2' C3' UMP sing 410 n n C2' H2' UMP sing 411 n n C2' "H2''" UMP sing 412 n n C3' C4' UMP sing 413 n n C3' O3' UMP sing 414 n n C3' H3' UMP sing 415 n n C4' O4' UMP sing 416 n n C4' C5' UMP sing 417 n n C4' H4' UMP sing 418 n n O3' HO3' UMP sing 419 n n C5' O5' UMP sing 420 n n C5' H5' UMP sing 421 n n C5' "H5''" UMP sing 422 n n O5' P UMP sing 423 n n P OP1 UMP doub 424 n n P OP2 UMP sing 425 n n P OP3 UMP sing 426 n n OP2 HOP2 UMP sing 427 n n OP3 HOP3 UMP sing 428 n n # _atom_sites.entry_id 6QXH _atom_sites.fract_transf_matrix[1][1] 0.005491 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.002605 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016236 _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] 0.010948 _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 D 2 UMP A 1 401 2 UMP UMP . E 3 PEG A 1 402 1 PEG PGE . F 4 CL A 1 403 1 CL CL . G 2 UMP B 1 401 1 UMP UMP . H 2 UMP C 1 401 3 UMP UMP . I 5 SO4 C 1 402 1 SO4 SO4 . J 6 HOH A 1 501 119 HOH HOH . J 6 HOH A 2 502 52 HOH HOH . J 6 HOH A 3 503 106 HOH HOH . J 6 HOH A 4 504 13 HOH HOH . J 6 HOH A 5 505 151 HOH HOH . J 6 HOH A 6 506 177 HOH HOH . J 6 HOH A 7 507 171 HOH HOH . J 6 HOH A 8 508 154 HOH HOH . J 6 HOH A 9 509 10 HOH HOH . J 6 HOH A 10 510 179 HOH HOH . J 6 HOH A 11 511 60 HOH HOH . J 6 HOH A 12 512 110 HOH HOH . J 6 HOH A 13 513 23 HOH HOH . J 6 HOH A 14 514 251 HOH HOH . J 6 HOH A 15 515 101 HOH HOH . J 6 HOH A 16 516 141 HOH HOH . J 6 HOH A 17 517 152 HOH HOH . J 6 HOH A 18 518 156 HOH HOH . J 6 HOH A 19 519 148 HOH HOH . J 6 HOH A 20 520 263 HOH HOH . J 6 HOH A 21 521 273 HOH HOH . J 6 HOH A 22 522 124 HOH HOH . J 6 HOH A 23 523 63 HOH HOH . J 6 HOH A 24 524 170 HOH HOH . J 6 HOH A 25 525 146 HOH HOH . J 6 HOH A 26 526 254 HOH HOH . J 6 HOH A 27 527 264 HOH HOH . J 6 HOH A 28 528 127 HOH HOH . J 6 HOH A 29 529 253 HOH HOH . J 6 HOH A 30 530 120 HOH HOH . J 6 HOH A 31 531 114 HOH HOH . J 6 HOH A 32 532 176 HOH HOH . J 6 HOH A 33 533 96 HOH HOH . J 6 HOH A 34 534 108 HOH HOH . J 6 HOH A 35 535 174 HOH HOH . J 6 HOH A 36 536 76 HOH HOH . J 6 HOH A 37 537 68 HOH HOH . J 6 HOH A 38 538 94 HOH HOH . J 6 HOH A 39 539 161 HOH HOH . J 6 HOH A 40 540 88 HOH HOH . J 6 HOH A 41 541 134 HOH HOH . J 6 HOH A 42 542 172 HOH HOH . J 6 HOH A 43 543 43 HOH HOH . J 6 HOH A 44 544 270 HOH HOH . J 6 HOH A 45 545 102 HOH HOH . J 6 HOH A 46 546 74 HOH HOH . J 6 HOH A 47 547 33 HOH HOH . J 6 HOH A 48 548 104 HOH HOH . J 6 HOH A 49 549 64 HOH HOH . J 6 HOH A 50 550 149 HOH HOH . J 6 HOH A 51 551 250 HOH HOH . J 6 HOH A 52 552 121 HOH HOH . J 6 HOH A 53 553 21 HOH HOH . J 6 HOH A 54 554 56 HOH HOH . J 6 HOH A 55 555 126 HOH HOH . J 6 HOH A 56 556 17 HOH HOH . J 6 HOH A 57 557 2 HOH HOH . J 6 HOH A 58 558 5 HOH HOH . J 6 HOH A 59 559 150 HOH HOH . J 6 HOH A 60 560 180 HOH HOH . J 6 HOH A 61 561 252 HOH HOH . J 6 HOH A 62 562 45 HOH HOH . J 6 HOH A 63 563 16 HOH HOH . J 6 HOH A 64 564 61 HOH HOH . J 6 HOH A 65 565 153 HOH HOH . J 6 HOH A 66 566 249 HOH HOH . K 6 HOH B 1 501 123 HOH HOH . K 6 HOH B 2 502 193 HOH HOH . K 6 HOH B 3 503 84 HOH HOH . K 6 HOH B 4 504 189 HOH HOH . K 6 HOH B 5 505 203 HOH HOH . K 6 HOH B 6 506 92 HOH HOH . K 6 HOH B 7 507 272 HOH HOH . K 6 HOH B 8 508 202 HOH HOH . K 6 HOH B 9 509 205 HOH HOH . K 6 HOH B 10 510 31 HOH HOH . K 6 HOH B 11 511 206 HOH HOH . K 6 HOH B 12 512 73 HOH HOH . K 6 HOH B 13 513 58 HOH HOH . K 6 HOH B 14 514 198 HOH HOH . K 6 HOH B 15 515 213 HOH HOH . K 6 HOH B 16 516 207 HOH HOH . K 6 HOH B 17 517 145 HOH HOH . K 6 HOH B 18 518 107 HOH HOH . K 6 HOH B 19 519 80 HOH HOH . K 6 HOH B 20 520 255 HOH HOH . K 6 HOH B 21 521 36 HOH HOH . K 6 HOH B 22 522 112 HOH HOH . K 6 HOH B 23 523 29 HOH HOH . K 6 HOH B 24 524 200 HOH HOH . K 6 HOH B 25 525 210 HOH HOH . K 6 HOH B 26 526 184 HOH HOH . K 6 HOH B 27 527 199 HOH HOH . K 6 HOH B 28 528 195 HOH HOH . K 6 HOH B 29 529 27 HOH HOH . K 6 HOH B 30 530 103 HOH HOH . K 6 HOH B 31 531 44 HOH HOH . K 6 HOH B 32 532 54 HOH HOH . K 6 HOH B 33 533 197 HOH HOH . K 6 HOH B 34 534 66 HOH HOH . K 6 HOH B 35 535 71 HOH HOH . K 6 HOH B 36 536 28 HOH HOH . K 6 HOH B 37 537 86 HOH HOH . K 6 HOH B 38 538 62 HOH HOH . K 6 HOH B 39 539 48 HOH HOH . K 6 HOH B 40 540 192 HOH HOH . K 6 HOH B 41 541 11 HOH HOH . K 6 HOH B 42 542 39 HOH HOH . K 6 HOH B 43 543 7 HOH HOH . K 6 HOH B 44 544 59 HOH HOH . K 6 HOH B 45 545 266 HOH HOH . K 6 HOH B 46 546 183 HOH HOH . K 6 HOH B 47 547 41 HOH HOH . K 6 HOH B 48 548 256 HOH HOH . K 6 HOH B 49 549 20 HOH HOH . K 6 HOH B 50 550 214 HOH HOH . K 6 HOH B 51 551 69 HOH HOH . K 6 HOH B 52 552 215 HOH HOH . K 6 HOH B 53 553 259 HOH HOH . K 6 HOH B 54 554 173 HOH HOH . K 6 HOH B 55 555 4 HOH HOH . K 6 HOH B 56 556 46 HOH HOH . K 6 HOH B 57 557 50 HOH HOH . K 6 HOH B 58 558 274 HOH HOH . K 6 HOH B 59 559 24 HOH HOH . K 6 HOH B 60 560 209 HOH HOH . K 6 HOH B 61 561 30 HOH HOH . K 6 HOH B 62 562 75 HOH HOH . K 6 HOH B 63 563 100 HOH HOH . L 6 HOH C 1 501 89 HOH HOH . L 6 HOH C 2 502 65 HOH HOH . L 6 HOH C 3 503 224 HOH HOH . L 6 HOH C 4 504 245 HOH HOH . L 6 HOH C 5 505 143 HOH HOH . L 6 HOH C 6 506 258 HOH HOH . L 6 HOH C 7 507 37 HOH HOH . L 6 HOH C 8 508 239 HOH HOH . L 6 HOH C 9 509 111 HOH HOH . L 6 HOH C 10 510 234 HOH HOH . L 6 HOH C 11 511 35 HOH HOH . L 6 HOH C 12 512 144 HOH HOH . L 6 HOH C 13 513 247 HOH HOH . L 6 HOH C 14 514 82 HOH HOH . L 6 HOH C 15 515 261 HOH HOH . L 6 HOH C 16 516 166 HOH HOH . L 6 HOH C 17 517 125 HOH HOH . L 6 HOH C 18 518 115 HOH HOH . L 6 HOH C 19 519 8 HOH HOH . L 6 HOH C 20 520 117 HOH HOH . L 6 HOH C 21 521 137 HOH HOH . L 6 HOH C 22 522 79 HOH HOH . L 6 HOH C 23 523 262 HOH HOH . L 6 HOH C 24 524 229 HOH HOH . L 6 HOH C 25 525 85 HOH HOH . L 6 HOH C 26 526 40 HOH HOH . L 6 HOH C 27 527 231 HOH HOH . L 6 HOH C 28 528 230 HOH HOH . L 6 HOH C 29 529 83 HOH HOH . L 6 HOH C 30 530 57 HOH HOH . L 6 HOH C 31 531 226 HOH HOH . L 6 HOH C 32 532 185 HOH HOH . L 6 HOH C 33 533 67 HOH HOH . L 6 HOH C 34 534 248 HOH HOH . L 6 HOH C 35 535 77 HOH HOH . L 6 HOH C 36 536 232 HOH HOH . L 6 HOH C 37 537 237 HOH HOH . L 6 HOH C 38 538 236 HOH HOH . L 6 HOH C 39 539 238 HOH HOH . L 6 HOH C 40 540 51 HOH HOH . L 6 HOH C 41 541 135 HOH HOH . L 6 HOH C 42 542 257 HOH HOH . L 6 HOH C 43 543 95 HOH HOH . L 6 HOH C 44 544 38 HOH HOH . L 6 HOH C 45 545 167 HOH HOH . L 6 HOH C 46 546 14 HOH HOH . L 6 HOH C 47 547 223 HOH HOH . L 6 HOH C 48 548 186 HOH HOH . L 6 HOH C 49 549 6 HOH HOH . L 6 HOH C 50 550 99 HOH HOH . L 6 HOH C 51 551 244 HOH HOH . L 6 HOH C 52 552 55 HOH HOH . L 6 HOH C 53 553 278 HOH HOH . L 6 HOH C 54 554 26 HOH HOH . L 6 HOH C 55 555 9 HOH HOH . L 6 HOH C 56 556 276 HOH HOH . L 6 HOH C 57 557 142 HOH HOH . L 6 HOH C 58 558 136 HOH HOH . L 6 HOH C 59 559 240 HOH HOH . L 6 HOH C 60 560 165 HOH HOH . L 6 HOH C 61 561 109 HOH HOH . L 6 HOH C 62 562 275 HOH HOH . L 6 HOH C 63 563 163 HOH HOH . L 6 HOH C 64 564 3 HOH HOH . L 6 HOH C 65 565 22 HOH HOH . L 6 HOH C 66 566 228 HOH HOH . L 6 HOH C 67 567 81 HOH HOH . L 6 HOH C 68 568 18 HOH HOH . L 6 HOH C 69 569 277 HOH HOH . L 6 HOH C 70 570 227 HOH HOH . L 6 HOH C 71 571 15 HOH HOH . L 6 HOH C 72 572 87 HOH HOH . L 6 HOH C 73 573 19 HOH HOH . L 6 HOH C 74 574 138 HOH HOH . L 6 HOH C 75 575 188 HOH HOH . L 6 HOH C 76 576 221 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 N N1 UMP . . . G 2 -57.827 16.618 31.447 1 62.65 ? N1 UMP 401 B 1 HETATM 2 C C2 UMP . . . G 2 -56.68 17.09 32.072 1 58.06 ? C2 UMP 401 B 1 HETATM 3 N N3 UMP . . . G 2 -56.368 16.473 33.258 1 59.48 ? N3 UMP 401 B 1 HETATM 4 C C4 UMP . . . G 2 -57.077 15.478 33.892 1 68.49 ? C4 UMP 401 B 1 HETATM 5 C C5 UMP . . . G 2 -58.267 15.044 33.202 1 69.49 ? C5 UMP 401 B 1 HETATM 6 C C6 UMP . . . G 2 -58.6 15.633 32.037 1 68.84 ? C6 UMP 401 B 1 HETATM 7 O O2 UMP . . . G 2 -55.962 17.967 31.62 1 56.37 ? O2 UMP 401 B 1 HETATM 8 O O4 UMP . . . G 2 -56.646 15.045 34.958 1 75.42 ? O4 UMP 401 B 1 HETATM 9 C C1' UMP . . . G 2 -58.299 17.275 30.199 1 61.3 ? C1' UMP 401 B 1 HETATM 10 C C2' UMP . . . G 2 -57.574 16.906 28.917 1 59.66 ? C2' UMP 401 B 1 HETATM 11 C C3' UMP . . . G 2 -58.69 17.034 27.886 1 64.98 ? C3' UMP 401 B 1 HETATM 12 C C4' UMP . . . G 2 -59.894 16.495 28.639 1 59.37 ? C4' UMP 401 B 1 HETATM 13 O O3' UMP . . . G 2 -58.91 18.411 27.588 1 64.2 ? O3' UMP 401 B 1 HETATM 14 O O4' UMP . . . G 2 -59.663 16.888 30.014 1 68.77 ? O4' UMP 401 B 1 HETATM 15 C C5' UMP . . . G 2 -60.091 15.002 28.541 1 63.11 ? C5' UMP 401 B 1 HETATM 16 O O5' UMP . . . G 2 -60.779 14.698 27.302 1 60.76 ? O5' UMP 401 B 1 HETATM 17 P P UMP . . . G 2 -60.181 13.65 26.246 1 61.8 ? P UMP 401 B 1 HETATM 18 O OP1 UMP . . . G 2 -58.686 13.906 26.107 1 62.88 ? OP1 UMP 401 B 1 HETATM 19 O OP2 UMP . . . G 2 -60.538 12.313 26.84 1 51.41 ? OP2 UMP 401 B 1 HETATM 20 O OP3 UMP . . . G 2 -60.895 13.902 24.903 1 67.6 ? OP3 UMP 401 B 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 17 _model_server_stats.query_time_ms 265 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 20 #