data_2NOM # _model_server_result.job_id w7JJzRvStJXkR3VQY_Oilw _model_server_result.datetime_utc '2025-06-19 12:27:48' _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":"E","auth_seq_id":501}' # _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 . . . E 3 -21.44 -2.018 -3.286 1 27.84 ? N1 DUT 501 A 1 HETATM 2 C C2 DUT . . . E 3 -22.624 -2.471 -2.651 1 29.98 ? C2 DUT 501 A 1 HETATM 3 N N3 DUT . . . E 3 -23.524 -1.544 -2.256 1 30.18 ? N3 DUT 501 A 1 HETATM 4 C C4 DUT . . . E 3 -23.301 -0.226 -2.437 1 28.65 ? C4 DUT 501 A 1 HETATM 5 C C5 DUT . . . E 3 -22.134 0.231 -3.036 1 28.51 ? C5 DUT 501 A 1 HETATM 6 C C6 DUT . . . E 3 -21.21 -0.698 -3.457 1 27.29 ? C6 DUT 501 A 1 HETATM 7 O O2 DUT . . . E 3 -22.866 -3.703 -2.462 1 31.08 ? O2 DUT 501 A 1 HETATM 8 O O4 DUT . . . E 3 -24.161 0.585 -2.052 1 29.9 ? O4 DUT 501 A 1 HETATM 9 C C1' DUT . . . E 3 -20.437 -2.987 -3.734 1 26.18 ? C1' DUT 501 A 1 HETATM 10 C C2' DUT . . . E 3 -20.88 -3.502 -5.092 1 21.13 ? C2' DUT 501 A 1 HETATM 11 C C3' DUT . . . E 3 -20.16 -2.548 -6.021 1 21.75 ? C3' DUT 501 A 1 HETATM 12 C C4' DUT . . . E 3 -18.844 -2.265 -5.286 1 22.27 ? C4' DUT 501 A 1 HETATM 13 O O4' DUT . . . E 3 -19.186 -2.296 -3.897 1 23.81 ? O4' DUT 501 A 1 HETATM 14 O O3' DUT . . . E 3 -20.045 -3.099 -7.334 1 19.04 ? O3' DUT 501 A 1 HETATM 15 C C5' DUT . . . E 3 -18.144 -0.938 -5.547 1 22.26 ? C5' DUT 501 A 1 HETATM 16 O O5' DUT . . . E 3 -19.028 0.109 -5.943 1 21.71 ? O5' DUT 501 A 1 HETATM 17 P PA DUT . . . E 3 -18.742 1.666 -5.599 1 15.9 ? PA DUT 501 A 1 HETATM 18 O O1A DUT . . . E 3 -17.973 1.766 -4.324 1 17.03 ? O1A DUT 501 A 1 HETATM 19 O O2A DUT . . . E 3 -20.053 2.447 -5.676 1 17.59 ? O2A DUT 501 A 1 HETATM 20 O O3A DUT . . . E 3 -17.999 2.232 -6.892 1 14.8 ? O3A DUT 501 A 1 HETATM 21 P PB DUT . . . E 3 -16.832 1.59 -7.751 1 18.62 ? PB DUT 501 A 1 HETATM 22 O O1B DUT . . . E 3 -15.695 1.245 -6.786 1 18.56 ? O1B DUT 501 A 1 HETATM 23 O O2B DUT . . . E 3 -17.436 0.483 -8.577 1 20.88 ? O2B DUT 501 A 1 HETATM 24 O O3B DUT . . . E 3 -16.479 2.803 -8.763 1 16.18 ? O3B DUT 501 A 1 HETATM 25 P PG DUT . . . E 3 -15.576 4.101 -8.37 1 14.24 ? PG DUT 501 A 1 HETATM 26 O O1G DUT . . . E 3 -16.58 5.136 -7.895 1 19.25 ? O1G DUT 501 A 1 HETATM 27 O O2G DUT . . . E 3 -14.913 4.5 -9.658 1 14.16 ? O2G DUT 501 A 1 HETATM 28 O O3G DUT . . . E 3 -14.647 3.59 -7.315 1 16.19 ? O3G DUT 501 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 8 _model_server_stats.query_time_ms 299 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 28 #