data_1DDU # _model_server_result.job_id fd3gK6jEwG0JVHzBaDp-5w _model_server_result.datetime_utc '2024-11-27 09:22:12' _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 1ddu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":533}' # _entry.id 1DDU # _exptl.entry_id 1DDU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 212.203 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-5'DIDEOXYURIDINE" _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 _cell.angle_gamma 120 _cell.entry_id 1DDU _cell.length_a 127.405 _cell.length_b 127.405 _cell.length_c 68.203 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1DDU _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 63' # _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,G,H,I,J _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 ? 3 D N N ? 3 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 covale ? covale1 A C FMT 1 A FMT 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? covale ? covale2 A O1 FMT 1 A FMT 0 1_555 A N MET 2 A MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.026 ? covale ? covale3 B C FMT 1 B FMT 0 1_555 B N MET 2 B MET 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.335 ? # _chem_comp.formula 'C9 H12 N2 O4' _chem_comp.formula_weight 212.203 _chem_comp.id DDU _chem_comp.mon_nstd_flag . _chem_comp.name "2'-5'DIDEOXYURIDINE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms ? # _atom_sites.entry_id 1DDU _atom_sites.fract_transf_matrix[1][1] 0.007849 _atom_sites.fract_transf_matrix[1][2] 0.004532 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.009063 _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] 0.014662 _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 PO4 A 1 530 530 PO4 PO4 . D 3 DDU A 1 532 532 DDU DDU . E 4 CB3 A 1 534 534 CB3 CB3 . F 2 PO4 B 1 531 531 PO4 PO4 . G 3 DDU B 1 533 533 DDU DDU . H 4 CB3 B 1 535 535 CB3 CB3 . I 5 HOH A 1 537 537 HOH HOH . I 5 HOH A 2 538 538 HOH HOH . I 5 HOH A 3 540 540 HOH HOH . I 5 HOH A 4 543 543 HOH HOH . I 5 HOH A 5 544 544 HOH HOH . I 5 HOH A 6 546 546 HOH HOH . I 5 HOH A 7 547 547 HOH HOH . I 5 HOH A 8 548 548 HOH HOH . I 5 HOH A 9 549 549 HOH HOH . I 5 HOH A 10 550 550 HOH HOH . I 5 HOH A 11 552 552 HOH HOH . I 5 HOH A 12 555 555 HOH HOH . I 5 HOH A 13 556 556 HOH HOH . I 5 HOH A 14 558 558 HOH HOH . I 5 HOH A 15 559 559 HOH HOH . I 5 HOH A 16 560 560 HOH HOH . I 5 HOH A 17 561 561 HOH HOH . I 5 HOH A 18 563 563 HOH HOH . I 5 HOH A 19 564 564 HOH HOH . I 5 HOH A 20 565 565 HOH HOH . I 5 HOH A 21 566 566 HOH HOH . I 5 HOH A 22 575 575 HOH HOH . I 5 HOH A 23 576 576 HOH HOH . I 5 HOH A 24 578 578 HOH HOH . I 5 HOH A 25 579 579 HOH HOH . I 5 HOH A 26 581 581 HOH HOH . I 5 HOH A 27 585 585 HOH HOH . I 5 HOH A 28 587 587 HOH HOH . I 5 HOH A 29 588 588 HOH HOH . I 5 HOH A 30 589 589 HOH HOH . I 5 HOH A 31 594 594 HOH HOH . I 5 HOH A 32 595 595 HOH HOH . I 5 HOH A 33 596 596 HOH HOH . I 5 HOH A 34 597 597 HOH HOH . I 5 HOH A 35 598 598 HOH HOH . I 5 HOH A 36 599 599 HOH HOH . I 5 HOH A 37 600 600 HOH HOH . I 5 HOH A 38 601 601 HOH HOH . I 5 HOH A 39 602 602 HOH HOH . J 5 HOH B 1 536 536 HOH HOH . J 5 HOH B 2 539 539 HOH HOH . J 5 HOH B 3 541 541 HOH HOH . J 5 HOH B 4 542 542 HOH HOH . J 5 HOH B 5 545 545 HOH HOH . J 5 HOH B 6 551 551 HOH HOH . J 5 HOH B 7 553 553 HOH HOH . J 5 HOH B 8 554 554 HOH HOH . J 5 HOH B 9 557 557 HOH HOH . J 5 HOH B 10 562 562 HOH HOH . J 5 HOH B 11 568 568 HOH HOH . J 5 HOH B 12 569 569 HOH HOH . J 5 HOH B 13 570 570 HOH HOH . J 5 HOH B 14 571 571 HOH HOH . J 5 HOH B 15 572 572 HOH HOH . J 5 HOH B 16 573 573 HOH HOH . J 5 HOH B 17 574 574 HOH HOH . J 5 HOH B 18 577 577 HOH HOH . J 5 HOH B 19 580 580 HOH HOH . J 5 HOH B 20 582 582 HOH HOH . J 5 HOH B 21 583 583 HOH HOH . J 5 HOH B 22 584 584 HOH HOH . J 5 HOH B 23 586 586 HOH HOH . J 5 HOH B 24 590 590 HOH HOH . J 5 HOH B 25 591 591 HOH HOH . J 5 HOH B 26 592 592 HOH HOH . J 5 HOH B 27 593 593 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 DDU . . . G 3 44.633 34.307 24.578 1 83.74 ? N1 DDU 533 B 1 HETATM 2 C C2 DDU . . . G 3 43.815 35.12 25.362 1 79.96 ? C2 DDU 533 B 1 HETATM 3 N N3 DDU . . . G 3 42.738 35.726 24.732 1 78.08 ? N3 DDU 533 B 1 HETATM 4 C C4 DDU . . . G 3 42.425 35.597 23.384 1 77.17 ? C4 DDU 533 B 1 HETATM 5 C C5 DDU . . . G 3 43.34 34.724 22.649 1 78.49 ? C5 DDU 533 B 1 HETATM 6 C C6 DDU . . . G 3 44.427 34.113 23.295 1 80.58 ? C6 DDU 533 B 1 HETATM 7 O O2 DDU . . . G 3 43.983 35.3 26.553 1 77.69 ? O2 DDU 533 B 1 HETATM 8 O O4 DDU . . . G 3 41.457 36.186 22.895 1 75.6 ? O4 DDU 533 B 1 HETATM 9 C C1' DDU . . . G 3 45.825 33.656 25.194 1 90.75 ? C1' DDU 533 B 1 HETATM 10 C C2' DDU . . . G 3 45.491 32.434 26.054 1 93.59 ? C2' DDU 533 B 1 HETATM 11 C C3' DDU . . . G 3 46.84 31.764 26.278 1 96.17 ? C3' DDU 533 B 1 HETATM 12 C C4' DDU . . . G 3 47.407 31.848 24.838 1 97.08 ? C4' DDU 533 B 1 HETATM 13 O O3' DDU . . . G 3 47.664 32.57 27.126 1 95.68 ? O3' DDU 533 B 1 HETATM 14 O O4' DDU . . . G 3 47.005 33.204 24.355 1 100 ? O4' DDU 533 B 1 HETATM 15 C C5' DDU . . . G 3 46.787 30.8 23.911 1 98.8 ? C5' DDU 533 B 1 # _model_server_stats.io_time_ms 5 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 253 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 15 #