data_2Q0F # _model_server_result.job_id AfKJXgXxXrRhQzghIUMO7w _model_server_result.datetime_utc '2024-11-16 11:28:54' _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 2q0f # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":502}' # _entry.id 2Q0F # _exptl.entry_id 2Q0F _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 324.181 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "URIDINE-5'-MONOPHOSPHATE" _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 94.37 _cell.angle_gamma 90 _cell.entry_id 2Q0F _cell.length_a 80.62 _cell.length_b 41.924 _cell.length_c 106.017 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2Q0F _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 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 ? monomeric 1 author_defined_assembly 1 ? monomeric 1 author_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,F,H 1 1 B,G,I 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 ? 4 F N N ? 4 G 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 metalc ? metalc1 A OD2 ASP 86 A ASP 66 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc2 A OD2 ASP 88 A ASP 68 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.182 ? metalc ? metalc3 C MG MG . A MG 401 1_555 E O1B UTP . A UTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc4 C MG MG . A MG 401 1_555 E O3G UTP . A UTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.538 ? metalc ? metalc5 C MG MG . A MG 401 1_555 E O1A UTP . A UTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.847 ? metalc ? metalc6 C MG MG . A MG 401 1_555 H O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.52 ? metalc ? metalc7 C MG MG . A MG 401 1_555 H O HOH . A HOH 574 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.422 ? metalc ? metalc8 D MG MG . A MG 402 1_555 E O1A UTP . A UTP 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc9 D MG MG . A MG 402 1_555 F O3' U5P . A U5P 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.572 ? metalc ? metalc10 D MG MG . A MG 402 1_555 H O HOH . A HOH 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.478 ? metalc ? metalc11 D MG MG . A MG 402 1_555 H O HOH . A HOH 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.609 ? metalc ? metalc12 D MG MG . A MG 402 1_555 H O HOH . A HOH 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.742 ? metalc ? metalc13 D MG MG . A MG 402 1_555 H O HOH . A HOH 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.285 ? # _chem_comp.formula 'C9 H13 N2 O9 P' _chem_comp.formula_weight 324.181 _chem_comp.id U5P _chem_comp.mon_nstd_flag . _chem_comp.name "URIDINE-5'-MONOPHOSPHATE" _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 N1 C2 U5P sing 358 n n N1 C6 U5P sing 359 n n N1 C1' U5P sing 360 n n C2 N3 U5P sing 361 n n C2 O2 U5P doub 362 n n N3 C4 U5P sing 363 n n N3 HN3 U5P sing 364 n n C4 C5 U5P sing 365 n n C4 O4 U5P doub 366 n n C5 C6 U5P doub 367 n n C5 H5 U5P sing 368 n n C6 H6 U5P sing 369 n n C1' C2' U5P sing 370 n n C1' O4' U5P sing 371 n n C1' H1' U5P sing 372 n n C2' O2' U5P sing 373 n n C2' C3' U5P sing 374 n n C2' H2' U5P sing 375 n n O2' HO2' U5P sing 376 n n C3' C4' U5P sing 377 n n C3' O3' U5P sing 378 n n C3' H3' U5P sing 379 n n C4' O4' U5P sing 380 n n C4' C5' U5P sing 381 n n C4' H4' U5P sing 382 n n O3' HO3' U5P sing 383 n n C5' O5' U5P sing 384 n n C5' "H5'1" U5P sing 385 n n C5' "H5'2" U5P sing 386 n n O5' P U5P sing 387 n n P O1P U5P doub 388 n n P O2P U5P sing 389 n n P O3P U5P sing 390 n n O2P HOP2 U5P sing 391 n n O3P HOP3 U5P sing 392 n n # _atom_sites.entry_id 2Q0F _atom_sites.fract_transf_matrix[1][1] 0.012404 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000947 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.023853 _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] 0.00946 _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 MG A 1 401 401 MG MG . D 2 MG A 1 402 402 MG MG . E 3 UTP A 1 501 501 UTP UTP . F 4 U5P A 1 502 502 U5P U5P . G 4 U5P B 1 503 503 U5P U5P . H 5 HOH A 1 503 1 HOH HOH . H 5 HOH A 2 504 2 HOH HOH . H 5 HOH A 3 505 3 HOH HOH . H 5 HOH A 4 506 4 HOH HOH . H 5 HOH A 5 507 5 HOH HOH . H 5 HOH A 6 508 6 HOH HOH . H 5 HOH A 7 509 7 HOH HOH . H 5 HOH A 8 510 8 HOH HOH . H 5 HOH A 9 511 9 HOH HOH . H 5 HOH A 10 512 11 HOH HOH . H 5 HOH A 11 513 12 HOH HOH . H 5 HOH A 12 514 14 HOH HOH . H 5 HOH A 13 515 15 HOH HOH . H 5 HOH A 14 516 16 HOH HOH . H 5 HOH A 15 517 19 HOH HOH . H 5 HOH A 16 518 21 HOH HOH . H 5 HOH A 17 519 23 HOH HOH . H 5 HOH A 18 520 24 HOH HOH . H 5 HOH A 19 521 26 HOH HOH . H 5 HOH A 20 522 27 HOH HOH . H 5 HOH A 21 523 29 HOH HOH . H 5 HOH A 22 524 30 HOH HOH . H 5 HOH A 23 525 31 HOH HOH . H 5 HOH A 24 526 32 HOH HOH . H 5 HOH A 25 527 34 HOH HOH . H 5 HOH A 26 528 36 HOH HOH . H 5 HOH A 27 529 37 HOH HOH . H 5 HOH A 28 530 38 HOH HOH . H 5 HOH A 29 531 40 HOH HOH . H 5 HOH A 30 532 41 HOH HOH . H 5 HOH A 31 533 42 HOH HOH . H 5 HOH A 32 534 43 HOH HOH . H 5 HOH A 33 535 46 HOH HOH . H 5 HOH A 34 536 47 HOH HOH . H 5 HOH A 35 537 48 HOH HOH . H 5 HOH A 36 538 50 HOH HOH . H 5 HOH A 37 539 51 HOH HOH . H 5 HOH A 38 540 52 HOH HOH . H 5 HOH A 39 541 59 HOH HOH . H 5 HOH A 40 542 62 HOH HOH . H 5 HOH A 41 543 63 HOH HOH . H 5 HOH A 42 544 64 HOH HOH . H 5 HOH A 43 545 67 HOH HOH . H 5 HOH A 44 546 69 HOH HOH . H 5 HOH A 45 547 70 HOH HOH . H 5 HOH A 46 548 73 HOH HOH . H 5 HOH A 47 549 76 HOH HOH . H 5 HOH A 48 550 77 HOH HOH . H 5 HOH A 49 551 79 HOH HOH . H 5 HOH A 50 552 80 HOH HOH . H 5 HOH A 51 553 83 HOH HOH . H 5 HOH A 52 554 85 HOH HOH . H 5 HOH A 53 555 87 HOH HOH . H 5 HOH A 54 556 89 HOH HOH . H 5 HOH A 55 557 91 HOH HOH . H 5 HOH A 56 558 94 HOH HOH . H 5 HOH A 57 559 98 HOH HOH . H 5 HOH A 58 560 99 HOH HOH . H 5 HOH A 59 561 100 HOH HOH . H 5 HOH A 60 562 101 HOH HOH . H 5 HOH A 61 563 103 HOH HOH . H 5 HOH A 62 564 105 HOH HOH . H 5 HOH A 63 565 106 HOH HOH . H 5 HOH A 64 566 107 HOH HOH . H 5 HOH A 65 567 108 HOH HOH . H 5 HOH A 66 568 109 HOH HOH . H 5 HOH A 67 569 112 HOH HOH . H 5 HOH A 68 570 113 HOH HOH . H 5 HOH A 69 571 114 HOH HOH . H 5 HOH A 70 572 115 HOH HOH . H 5 HOH A 71 573 118 HOH HOH . H 5 HOH A 72 574 121 HOH HOH . H 5 HOH A 73 575 125 HOH HOH . H 5 HOH A 74 576 126 HOH HOH . H 5 HOH A 75 577 127 HOH HOH . H 5 HOH A 76 578 128 HOH HOH . H 5 HOH A 77 579 129 HOH HOH . H 5 HOH A 78 580 133 HOH HOH . H 5 HOH A 79 581 134 HOH HOH . H 5 HOH A 80 582 136 HOH HOH . H 5 HOH A 81 583 138 HOH HOH . H 5 HOH A 82 584 139 HOH HOH . H 5 HOH A 83 585 140 HOH HOH . H 5 HOH A 84 586 141 HOH HOH . H 5 HOH A 85 587 144 HOH HOH . H 5 HOH A 86 588 146 HOH HOH . H 5 HOH A 87 589 147 HOH HOH . H 5 HOH A 88 590 148 HOH HOH . H 5 HOH A 89 591 149 HOH HOH . H 5 HOH A 90 592 150 HOH HOH . H 5 HOH A 91 593 151 HOH HOH . H 5 HOH A 92 594 152 HOH HOH . H 5 HOH A 93 595 153 HOH HOH . H 5 HOH A 94 596 157 HOH HOH . H 5 HOH A 95 597 162 HOH HOH . H 5 HOH A 96 598 163 HOH HOH . H 5 HOH A 97 599 164 HOH HOH . H 5 HOH A 98 600 165 HOH HOH . H 5 HOH A 99 601 167 HOH HOH . H 5 HOH A 100 602 168 HOH HOH . H 5 HOH A 101 603 171 HOH HOH . H 5 HOH A 102 604 172 HOH HOH . H 5 HOH A 103 605 173 HOH HOH . H 5 HOH A 104 606 174 HOH HOH . H 5 HOH A 105 607 175 HOH HOH . H 5 HOH A 106 608 176 HOH HOH . H 5 HOH A 107 609 177 HOH HOH . H 5 HOH A 108 610 178 HOH HOH . H 5 HOH A 109 611 179 HOH HOH . H 5 HOH A 110 612 181 HOH HOH . H 5 HOH A 111 613 182 HOH HOH . I 5 HOH B 1 504 10 HOH HOH . I 5 HOH B 2 505 13 HOH HOH . I 5 HOH B 3 506 17 HOH HOH . I 5 HOH B 4 507 18 HOH HOH . I 5 HOH B 5 508 20 HOH HOH . I 5 HOH B 6 509 22 HOH HOH . I 5 HOH B 7 510 25 HOH HOH . I 5 HOH B 8 511 28 HOH HOH . I 5 HOH B 9 512 33 HOH HOH . I 5 HOH B 10 513 35 HOH HOH . I 5 HOH B 11 514 39 HOH HOH . I 5 HOH B 12 515 44 HOH HOH . I 5 HOH B 13 516 45 HOH HOH . I 5 HOH B 14 517 49 HOH HOH . I 5 HOH B 15 518 53 HOH HOH . I 5 HOH B 16 519 54 HOH HOH . I 5 HOH B 17 520 55 HOH HOH . I 5 HOH B 18 521 56 HOH HOH . I 5 HOH B 19 522 57 HOH HOH . I 5 HOH B 20 523 58 HOH HOH . I 5 HOH B 21 524 60 HOH HOH . I 5 HOH B 22 525 61 HOH HOH . I 5 HOH B 23 526 65 HOH HOH . I 5 HOH B 24 527 66 HOH HOH . I 5 HOH B 25 528 68 HOH HOH . I 5 HOH B 26 529 71 HOH HOH . I 5 HOH B 27 530 72 HOH HOH . I 5 HOH B 28 531 74 HOH HOH . I 5 HOH B 29 532 75 HOH HOH . I 5 HOH B 30 533 78 HOH HOH . I 5 HOH B 31 534 81 HOH HOH . I 5 HOH B 32 535 82 HOH HOH . I 5 HOH B 33 536 84 HOH HOH . I 5 HOH B 34 537 86 HOH HOH . I 5 HOH B 35 538 88 HOH HOH . I 5 HOH B 36 539 90 HOH HOH . I 5 HOH B 37 540 92 HOH HOH . I 5 HOH B 38 541 93 HOH HOH . I 5 HOH B 39 542 95 HOH HOH . I 5 HOH B 40 543 96 HOH HOH . I 5 HOH B 41 544 97 HOH HOH . I 5 HOH B 42 545 102 HOH HOH . I 5 HOH B 43 546 104 HOH HOH . I 5 HOH B 44 547 110 HOH HOH . I 5 HOH B 45 548 111 HOH HOH . I 5 HOH B 46 549 116 HOH HOH . I 5 HOH B 47 550 117 HOH HOH . I 5 HOH B 48 551 119 HOH HOH . I 5 HOH B 49 552 120 HOH HOH . I 5 HOH B 50 553 122 HOH HOH . I 5 HOH B 51 554 123 HOH HOH . I 5 HOH B 52 555 124 HOH HOH . I 5 HOH B 53 556 130 HOH HOH . I 5 HOH B 54 557 131 HOH HOH . I 5 HOH B 55 558 132 HOH HOH . I 5 HOH B 56 559 135 HOH HOH . I 5 HOH B 57 560 137 HOH HOH . I 5 HOH B 58 561 142 HOH HOH . I 5 HOH B 59 562 143 HOH HOH . I 5 HOH B 60 563 145 HOH HOH . I 5 HOH B 61 564 154 HOH HOH . I 5 HOH B 62 565 155 HOH HOH . I 5 HOH B 63 566 156 HOH HOH . I 5 HOH B 64 567 158 HOH HOH . I 5 HOH B 65 568 159 HOH HOH . I 5 HOH B 66 569 160 HOH HOH . I 5 HOH B 67 570 161 HOH HOH . I 5 HOH B 68 571 166 HOH HOH . I 5 HOH B 69 572 169 HOH HOH . I 5 HOH B 70 573 170 HOH HOH . I 5 HOH B 71 574 180 HOH HOH . I 5 HOH B 72 575 183 HOH HOH . I 5 HOH B 73 576 184 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 U5P . . . F 4 24.016 21.778 -54.155 1 52.3 ? N1 U5P 502 A 1 HETATM 2 C C2 U5P . . . F 4 24.254 20.377 -54.017 1 51.57 ? C2 U5P 502 A 1 HETATM 3 N N3 U5P . . . F 4 25.501 19.905 -53.957 1 51.44 ? N3 U5P 502 A 1 HETATM 4 C C4 U5P . . . F 4 26.561 20.721 -54.027 1 52.2 ? C4 U5P 502 A 1 HETATM 5 C C5 U5P . . . F 4 26.398 22.103 -54.158 1 52.82 ? C5 U5P 502 A 1 HETATM 6 C C6 U5P . . . F 4 25.092 22.603 -54.224 1 53.08 ? C6 U5P 502 A 1 HETATM 7 O O2 U5P . . . F 4 23.322 19.549 -53.948 1 52.89 ? O2 U5P 502 A 1 HETATM 8 O O4 U5P . . . F 4 27.701 20.225 -53.961 1 52.64 ? O4 U5P 502 A 1 HETATM 9 C C1' U5P . . . F 4 22.628 22.319 -54.241 1 51.57 ? C1' U5P 502 A 1 HETATM 10 C C2' U5P . . . F 4 21.986 22.552 -52.884 1 50.85 ? C2' U5P 502 A 1 HETATM 11 O O2' U5P . . . F 4 20.611 22.155 -52.986 1 49.55 ? O2' U5P 502 A 1 HETATM 12 C C3' U5P . . . F 4 22.161 24.048 -52.646 1 49.83 ? C3' U5P 502 A 1 HETATM 13 C C4' U5P . . . F 4 22.192 24.649 -54.05 1 50.31 ? C4' U5P 502 A 1 HETATM 14 O O3' U5P . . . F 4 21.135 24.613 -51.815 1 48.9 ? O3' U5P 502 A 1 HETATM 15 O O4' U5P . . . F 4 22.572 23.583 -54.929 1 51.55 ? O4' U5P 502 A 1 HETATM 16 C C5' U5P . . . F 4 23.153 25.829 -54.218 1 49.99 ? C5' U5P 502 A 1 HETATM 17 O O5' U5P . . . F 4 24.534 25.457 -54.054 1 49.1 ? O5' U5P 502 A 1 HETATM 18 P P U5P . . . F 4 25.594 26.514 -53.425 1 49.39 ? P U5P 502 A 1 HETATM 19 O O1P U5P . . . F 4 25.4 27.707 -54.357 1 49.38 ? O1P U5P 502 A 1 HETATM 20 O O2P U5P . . . F 4 26.95 25.834 -53.527 1 48.69 ? O2P U5P 502 A 1 HETATM 21 O O3P U5P . . . F 4 25.146 26.765 -51.99 1 47.54 ? O3P U5P 502 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 15 _model_server_stats.create_model_time_ms 9 _model_server_stats.query_time_ms 290 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 21 #