data_2NOM # _model_server_result.job_id zVFIFgyfgjgaY5jPYuo3WA _model_server_result.datetime_utc '2025-06-19 12:57:32' _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 2nom # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":502}' # _entry.id 2NOM # _exptl.entry_id 2NOM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 468.142 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "DEOXYURIDINE-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 96.46 _cell.angle_gamma 90 _cell.entry_id 2NOM _cell.length_a 79.142 _cell.length_b 41.659 _cell.length_c 104.286 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2NOM _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,G 1 1 B,F,H 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 metalc ? metalc1 A OD2 ASP 86 A ASP 66 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc2 A OD1 ASP 86 A ASP 66 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.351 ? metalc ? metalc3 A OD2 ASP 86 A ASP 66 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.974 ? metalc ? metalc4 A OD2 ASP 88 A ASP 68 1_555 C MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.241 ? metalc ? metalc5 A OD1 ASP 88 A ASP 68 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc6 A OD2 ASP 88 A ASP 68 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.894 ? metalc ? metalc7 A OD2 ASP 156 A ASP 136 1_555 D MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.237 ? metalc ? metalc8 C MG MG . A MG 401 1_555 E O1B DUT . A DUT 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.314 ? metalc ? metalc9 C MG MG . A MG 401 1_555 E O3G DUT . A DUT 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc10 C MG MG . A MG 401 1_555 G O HOH . A HOH 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.881 ? metalc ? metalc11 C MG MG . A MG 401 1_555 G O HOH . A HOH 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.489 ? metalc ? metalc12 D MG MG . A MG 402 1_555 G O HOH . A HOH 588 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.37 ? metalc ? metalc13 D MG MG . A MG 402 1_555 G O HOH . A HOH 589 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.357 ? metalc ? metalc14 D MG MG . A MG 402 1_555 G O HOH . A HOH 590 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.129 ? # _chem_comp.formula 'C9 H15 N2 O14 P3' _chem_comp.formula_weight 468.142 _chem_comp.id DUT _chem_comp.mon_nstd_flag . _chem_comp.name "DEOXYURIDINE-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 N1 C2 DUT sing 83 n n N1 C6 DUT sing 84 n n N1 C1' DUT sing 85 n n C2 N3 DUT sing 86 n n C2 O2 DUT doub 87 n n N3 C4 DUT sing 88 n n N3 HN3 DUT sing 89 n n C4 C5 DUT sing 90 n n C4 O4 DUT doub 91 n n C5 C6 DUT doub 92 n n C5 H5 DUT sing 93 n n C6 H6 DUT sing 94 n n C1' C2' DUT sing 95 n n C1' O4' DUT sing 96 n n C1' H1' DUT sing 97 n n C2' C3' DUT sing 98 n n C2' "H2'1" DUT sing 99 n n C2' "H2'2" DUT sing 100 n n C3' C4' DUT sing 101 n n C3' O3' DUT sing 102 n n C3' H3' DUT sing 103 n n C4' O4' DUT sing 104 n n C4' C5' DUT sing 105 n n C4' H4' DUT sing 106 n n O3' HO3' DUT sing 107 n n C5' O5' DUT sing 108 n n C5' "H5'1" DUT sing 109 n n C5' "H5'2" DUT sing 110 n n O5' PA DUT sing 111 n n PA O1A DUT doub 112 n n PA O2A DUT sing 113 n n PA O3A DUT sing 114 n n O2A HOA2 DUT sing 115 n n O3A PB DUT sing 116 n n PB O1B DUT doub 117 n n PB O2B DUT sing 118 n n PB O3B DUT sing 119 n n O2B HOB2 DUT sing 120 n n O3B PG DUT sing 121 n n PG O1G DUT doub 122 n n PG O2G DUT sing 123 n n PG O3G DUT sing 124 n n O2G HOG2 DUT sing 125 n n O3G HOG3 DUT sing 126 n n # _atom_sites.entry_id 2NOM _atom_sites.fract_transf_matrix[1][1] 0.012636 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00143 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.024004 _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] 0.00965 _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 DUT A 1 501 501 DUT DUT . F 3 DUT B 1 502 502 DUT DUT . G 4 HOH A 1 502 1 HOH HOH . G 4 HOH A 2 503 3 HOH HOH . G 4 HOH A 3 504 4 HOH HOH . G 4 HOH A 4 505 5 HOH HOH . G 4 HOH A 5 506 6 HOH HOH . G 4 HOH A 6 507 7 HOH HOH . G 4 HOH A 7 508 8 HOH HOH . G 4 HOH A 8 509 9 HOH HOH . G 4 HOH A 9 510 10 HOH HOH . G 4 HOH A 10 511 11 HOH HOH . G 4 HOH A 11 512 12 HOH HOH . G 4 HOH A 12 513 13 HOH HOH . G 4 HOH A 13 514 14 HOH HOH . G 4 HOH A 14 515 15 HOH HOH . G 4 HOH A 15 516 16 HOH HOH . G 4 HOH A 16 517 17 HOH HOH . G 4 HOH A 17 518 18 HOH HOH . G 4 HOH A 18 519 22 HOH HOH . G 4 HOH A 19 520 23 HOH HOH . G 4 HOH A 20 521 24 HOH HOH . G 4 HOH A 21 522 25 HOH HOH . G 4 HOH A 22 523 26 HOH HOH . G 4 HOH A 23 524 27 HOH HOH . G 4 HOH A 24 525 28 HOH HOH . G 4 HOH A 25 526 29 HOH HOH . G 4 HOH A 26 527 31 HOH HOH . G 4 HOH A 27 528 33 HOH HOH . G 4 HOH A 28 529 34 HOH HOH . G 4 HOH A 29 530 35 HOH HOH . G 4 HOH A 30 531 36 HOH HOH . G 4 HOH A 31 532 37 HOH HOH . G 4 HOH A 32 533 39 HOH HOH . G 4 HOH A 33 534 40 HOH HOH . G 4 HOH A 34 535 41 HOH HOH . G 4 HOH A 35 536 42 HOH HOH . G 4 HOH A 36 537 43 HOH HOH . G 4 HOH A 37 538 45 HOH HOH . G 4 HOH A 38 539 46 HOH HOH . G 4 HOH A 39 540 47 HOH HOH . G 4 HOH A 40 541 48 HOH HOH . G 4 HOH A 41 542 50 HOH HOH . G 4 HOH A 42 543 52 HOH HOH . G 4 HOH A 43 544 53 HOH HOH . G 4 HOH A 44 545 54 HOH HOH . G 4 HOH A 45 546 55 HOH HOH . G 4 HOH A 46 547 56 HOH HOH . G 4 HOH A 47 548 57 HOH HOH . G 4 HOH A 48 549 59 HOH HOH . G 4 HOH A 49 550 60 HOH HOH . G 4 HOH A 50 551 61 HOH HOH . G 4 HOH A 51 552 64 HOH HOH . G 4 HOH A 52 553 66 HOH HOH . G 4 HOH A 53 554 70 HOH HOH . G 4 HOH A 54 555 71 HOH HOH . G 4 HOH A 55 556 73 HOH HOH . G 4 HOH A 56 557 74 HOH HOH . G 4 HOH A 57 558 75 HOH HOH . G 4 HOH A 58 559 76 HOH HOH . G 4 HOH A 59 560 77 HOH HOH . G 4 HOH A 60 561 78 HOH HOH . G 4 HOH A 61 562 79 HOH HOH . G 4 HOH A 62 563 80 HOH HOH . G 4 HOH A 63 564 81 HOH HOH . G 4 HOH A 64 565 83 HOH HOH . G 4 HOH A 65 566 84 HOH HOH . G 4 HOH A 66 567 86 HOH HOH . G 4 HOH A 67 568 87 HOH HOH . G 4 HOH A 68 569 89 HOH HOH . G 4 HOH A 69 570 90 HOH HOH . G 4 HOH A 70 571 92 HOH HOH . G 4 HOH A 71 572 93 HOH HOH . G 4 HOH A 72 573 96 HOH HOH . G 4 HOH A 73 574 99 HOH HOH . G 4 HOH A 74 575 100 HOH HOH . G 4 HOH A 75 576 102 HOH HOH . G 4 HOH A 76 577 103 HOH HOH . G 4 HOH A 77 578 104 HOH HOH . G 4 HOH A 78 579 106 HOH HOH . G 4 HOH A 79 580 107 HOH HOH . G 4 HOH A 80 581 108 HOH HOH . G 4 HOH A 81 582 109 HOH HOH . G 4 HOH A 82 583 110 HOH HOH . G 4 HOH A 83 584 112 HOH HOH . G 4 HOH A 84 585 113 HOH HOH . G 4 HOH A 85 586 114 HOH HOH . G 4 HOH A 86 587 115 HOH HOH . G 4 HOH A 87 588 117 HOH HOH . G 4 HOH A 88 589 118 HOH HOH . G 4 HOH A 89 590 119 HOH HOH . G 4 HOH A 90 591 120 HOH HOH . G 4 HOH A 91 592 121 HOH HOH . G 4 HOH A 92 593 122 HOH HOH . G 4 HOH A 93 594 123 HOH HOH . G 4 HOH A 94 595 124 HOH HOH . H 4 HOH B 1 503 2 HOH HOH . H 4 HOH B 2 504 19 HOH HOH . H 4 HOH B 3 505 20 HOH HOH . H 4 HOH B 4 506 21 HOH HOH . H 4 HOH B 5 507 30 HOH HOH . H 4 HOH B 6 508 32 HOH HOH . H 4 HOH B 7 509 38 HOH HOH . H 4 HOH B 8 510 44 HOH HOH . H 4 HOH B 9 511 49 HOH HOH . H 4 HOH B 10 512 51 HOH HOH . H 4 HOH B 11 513 58 HOH HOH . H 4 HOH B 12 514 62 HOH HOH . H 4 HOH B 13 515 63 HOH HOH . H 4 HOH B 14 516 65 HOH HOH . H 4 HOH B 15 517 67 HOH HOH . H 4 HOH B 16 518 68 HOH HOH . H 4 HOH B 17 519 69 HOH HOH . H 4 HOH B 18 520 72 HOH HOH . H 4 HOH B 19 521 82 HOH HOH . H 4 HOH B 20 522 85 HOH HOH . H 4 HOH B 21 523 88 HOH HOH . H 4 HOH B 22 524 91 HOH HOH . H 4 HOH B 23 525 94 HOH HOH . H 4 HOH B 24 526 95 HOH HOH . H 4 HOH B 25 527 97 HOH HOH . H 4 HOH B 26 528 98 HOH HOH . H 4 HOH B 27 529 101 HOH HOH . H 4 HOH B 28 530 105 HOH HOH . H 4 HOH B 29 531 111 HOH HOH . H 4 HOH B 30 532 116 HOH HOH . H 4 HOH B 31 533 125 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 DUT . . . F 3 -20.914 10.875 36.662 0.5 50.15 ? N1 DUT 502 B 1 HETATM 2 C C2 DUT . . . F 3 -21.569 11.539 35.584 0.5 50.23 ? C2 DUT 502 B 1 HETATM 3 N N3 DUT . . . F 3 -21.081 12.709 35.094 0.5 50.37 ? N3 DUT 502 B 1 HETATM 4 C C4 DUT . . . F 3 -19.96 13.267 35.623 0.5 50.24 ? C4 DUT 502 B 1 HETATM 5 C C5 DUT . . . F 3 -19.305 12.634 36.679 0.5 50.09 ? C5 DUT 502 B 1 HETATM 6 C C6 DUT . . . F 3 -19.804 11.436 37.185 0.5 50.2 ? C6 DUT 502 B 1 HETATM 7 O O2 DUT . . . F 3 -22.604 11.06 35.071 0.5 50.2 ? O2 DUT 502 B 1 HETATM 8 O O4 DUT . . . F 3 -19.512 14.343 35.165 0.5 49.86 ? O4 DUT 502 B 1 HETATM 9 C C1' DUT . . . F 3 -21.441 9.6 37.197 0.5 49.86 ? C1' DUT 502 B 1 HETATM 10 C C2' DUT . . . F 3 -20.607 8.436 36.689 0.5 49.63 ? C2' DUT 502 B 1 HETATM 11 C C3' DUT . . . F 3 -19.883 7.865 37.898 0.5 49.68 ? C3' DUT 502 B 1 HETATM 12 C C4' DUT . . . F 3 -20.504 8.526 39.119 0.5 50.37 ? C4' DUT 502 B 1 HETATM 13 O O4' DUT . . . F 3 -21.393 9.542 38.629 0.5 50.37 ? O4' DUT 502 B 1 HETATM 14 O O3' DUT . . . F 3 -20 6.439 37.941 0.5 49.2 ? O3' DUT 502 B 1 HETATM 15 C C5' DUT . . . F 3 -19.419 9.177 39.977 0.5 50.84 ? C5' DUT 502 B 1 HETATM 16 O O5' DUT . . . F 3 -19.791 9.331 41.35 0.5 50.69 ? O5' DUT 502 B 1 HETATM 17 P PA DUT . . . F 3 -18.863 10.223 42.338 0.5 50.76 ? PA DUT 502 B 1 HETATM 18 O O1A DUT . . . F 3 -19.426 10.139 43.737 0.5 51.62 ? O1A DUT 502 B 1 HETATM 19 O O2A DUT . . . F 3 -18.648 11.589 41.728 0.5 50.43 ? O2A DUT 502 B 1 HETATM 20 O O3A DUT . . . F 3 -17.441 9.476 42.336 0.5 50.2 ? O3A DUT 502 B 1 HETATM 21 P PB DUT . . . F 3 -17.267 8.059 43.071 0.5 50.54 ? PB DUT 502 B 1 HETATM 22 O O1B DUT . . . F 3 -17.42 8.249 44.561 0.5 50.04 ? O1B DUT 502 B 1 HETATM 23 O O2B DUT . . . F 3 -18.168 7.069 42.382 0.5 50.25 ? O2B DUT 502 B 1 HETATM 24 O O3B DUT . . . F 3 -15.735 7.687 42.709 0.5 48.61 ? O3B DUT 502 B 1 HETATM 25 P PG DUT . . . F 3 -14.452 8.403 43.378 0.5 46.63 ? PG DUT 502 B 1 HETATM 26 O O1G DUT . . . F 3 -13.57 8.727 42.195 0.5 46.59 ? O1G DUT 502 B 1 HETATM 27 O O2G DUT . . . F 3 -13.9 7.346 44.309 0.5 44.79 ? O2G DUT 502 B 1 HETATM 28 O O3G DUT . . . F 3 -14.978 9.644 44.047 0.5 45.6 ? O3G DUT 502 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 296 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #