data_1DDU # _model_server_result.job_id wC4WRt9OsiaDHWZOWlX4vQ _model_server_result.datetime_utc '2024-10-19 05:32:22' _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":"H","auth_seq_id":535}' # _entry.id 1DDU # _exptl.entry_id 1DDU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 477.469 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '10-PROPARGYL-5,8-DIDEAZAFOLIC ACID' _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 ? 4 E N N ? 4 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 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 'C24 H23 N5 O6' _chem_comp.formula_weight 477.469 _chem_comp.id CB3 _chem_comp.mon_nstd_flag . _chem_comp.name '10-PROPARGYL-5,8-DIDEAZAFOLIC ACID' _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 CB3 . . . H 4 48.803 34.895 23.276 1 66.64 ? N1 CB3 535 B 1 HETATM 2 C C2 CB3 . . . H 4 49.149 35.348 24.496 1 65.78 ? C2 CB3 535 B 1 HETATM 3 N NA2 CB3 . . . H 4 50.284 34.953 25.051 1 66.15 ? NA2 CB3 535 B 1 HETATM 4 N N3 CB3 . . . H 4 48.371 36.237 25.135 1 65.32 ? N3 CB3 535 B 1 HETATM 5 C C4 CB3 . . . H 4 47.327 36.822 24.528 1 65.11 ? C4 CB3 535 B 1 HETATM 6 O O4 CB3 . . . H 4 46.581 37.733 25.24 1 64.49 ? O4 CB3 535 B 1 HETATM 7 C C4A CB3 . . . H 4 47.018 36.483 23.205 1 65.72 ? C4A CB3 535 B 1 HETATM 8 C C5 CB3 . . . H 4 46.009 37.12 22.471 1 66.58 ? C5 CB3 535 B 1 HETATM 9 C C6 CB3 . . . H 4 45.704 36.711 21.153 1 67.87 ? C6 CB3 535 B 1 HETATM 10 C C7 CB3 . . . H 4 46.405 35.629 20.604 1 67.12 ? C7 CB3 535 B 1 HETATM 11 C C8 CB3 . . . H 4 47.429 35.004 21.327 1 66.07 ? C8 CB3 535 B 1 HETATM 12 C C8A CB3 . . . H 4 47.756 35.439 22.615 1 66.28 ? C8A CB3 535 B 1 HETATM 13 C C9 CB3 . . . H 4 44.826 37.475 20.228 1 70.14 ? C9 CB3 535 B 1 HETATM 14 N N10 CB3 . . . H 4 44.352 38.797 20.691 1 73.26 ? N10 CB3 535 B 1 HETATM 15 C C11 CB3 . . . H 4 47.048 41.631 22.028 1 90.03 ? C11 CB3 535 B 1 HETATM 16 C C12 CB3 . . . H 4 45.892 41.391 22.758 1 86.95 ? C12 CB3 535 B 1 HETATM 17 C C13 CB3 . . . H 4 44.966 40.46 22.276 1 83.04 ? C13 CB3 535 B 1 HETATM 18 C C14 CB3 . . . H 4 45.197 39.773 21.07 1 79.14 ? C14 CB3 535 B 1 HETATM 19 C C15 CB3 . . . H 4 46.353 40.068 20.323 1 82.95 ? C15 CB3 535 B 1 HETATM 20 C C16 CB3 . . . H 4 47.283 40.999 20.803 1 86.96 ? C16 CB3 535 B 1 HETATM 21 C C CB3 . . . H 4 48.042 42.506 22.574 1 93.41 ? C CB3 535 B 1 HETATM 22 O O CB3 . . . H 4 49.245 42.189 22.585 1 94.53 ? O CB3 535 B 1 HETATM 23 N N CB3 . . . H 4 47.59 43.737 23.025 1 100 ? N CB3 535 B 1 HETATM 24 C CA CB3 . . . H 4 48.63 44.838 23.208 1 95.07 ? CA CB3 535 B 1 HETATM 25 C CB CB3 . . . H 4 48.951 45.532 21.857 1 93.09 ? CB CB3 535 B 1 HETATM 26 C CG CB3 . . . H 4 47.735 45.731 20.957 1 89.73 ? CG CB3 535 B 1 HETATM 27 C CD CB3 . . . H 4 47.385 47.171 20.608 1 87.7 ? CD CB3 535 B 1 HETATM 28 O OE1 CB3 . . . H 4 46.193 47.493 20.555 1 86.49 ? OE1 CB3 535 B 1 HETATM 29 O OE2 CB3 . . . H 4 48.297 47.964 20.364 1 86.72 ? OE2 CB3 535 B 1 HETATM 30 C CT CB3 . . . H 4 48.213 45.896 24.198 1 95.46 ? CT CB3 535 B 1 HETATM 31 O O1 CB3 . . . H 4 49.085 46.311 24.955 1 94.48 ? O1 CB3 535 B 1 HETATM 32 O O2 CB3 . . . H 4 47.037 46.244 24.234 1 95.46 ? O2 CB3 535 B 1 HETATM 33 C CP1 CB3 . . . H 4 42.904 38.997 20.778 1 69.49 ? CP1 CB3 535 B 1 HETATM 34 C CP2 CB3 . . . H 4 42.478 38.858 22.162 1 66 ? CP2 CB3 535 B 1 HETATM 35 C CP3 CB3 . . . H 4 42.274 38.712 23.333 1 63.86 ? CP3 CB3 535 B 1 # _model_server_stats.io_time_ms 16 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 33 _model_server_stats.query_time_ms 326 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 35 #