data_5Y7T # _model_server_result.job_id mR3pRWdW3RH02NHvTgr6Ag _model_server_result.datetime_utc '2024-10-18 12:23:28' _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 5y7t # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":402}' # _entry.id 5Y7T # _exptl.entry_id 5Y7T _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 280.321 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3R)-4-methyl-3-(phenylmethyl)-1,3-dihydro-1,4-benzodiazepine-2,5-dione _entity.pdbx_number_of_molecules 1 _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 90 _cell.entry_id 5Y7T _cell.length_a 73.471 _cell.length_b 118.619 _cell.length_c 66.427 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5Y7T _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 2 2 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag 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 NE2 HIS 141 B HIS 134 1_555 B FE FE . B FE 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.263 ? metalc ? metalc2 A OD1 ASP 143 B ASP 136 1_555 B FE FE . B FE 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc3 A NE2 HIS 218 B HIS 211 1_555 B FE FE . B FE 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.21 ? metalc ? metalc4 B FE FE . B FE 401 1_555 D O1 AKG . B AKG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.012 ? metalc ? metalc5 B FE FE . B FE 401 1_555 D O5 AKG . B AKG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.221 ? metalc ? metalc6 B FE FE . B FE 401 1_555 E O HOH . B HOH 501 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.013 ? # _chem_comp.formula 'C17 H16 N2 O2' _chem_comp.formula_weight 280.321 _chem_comp.id 8R0 _chem_comp.mon_nstd_flag . _chem_comp.name (3R)-4-methyl-3-(phenylmethyl)-1,3-dihydro-1,4-benzodiazepine-2,5-dione _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 C20 C19 8R0 doub 1 n y C20 C1 8R0 sing 2 n y C19 C18 8R0 sing 3 n y N17 C18 8R0 sing 4 n n N17 C15 8R0 sing 5 n n C18 C3 8R0 doub 6 n y C1 C2 8R0 doub 7 n y O16 C15 8R0 doub 8 n n C15 C7 8R0 sing 9 n n C2 C3 8R0 sing 10 n y C3 C4 8R0 sing 11 n n C7 C8 8R0 sing 12 n n C7 N6 8R0 sing 13 n n C8 C9 8R0 sing 14 n n C4 N6 8R0 sing 15 n n C4 O5 8R0 doub 16 n n N6 C23 8R0 sing 17 n n C9 C14 8R0 doub 18 n y C9 C10 8R0 sing 19 n y C14 C13 8R0 sing 20 n y C10 C11 8R0 doub 21 n y C13 C12 8R0 doub 22 n y C11 C12 8R0 sing 23 n y C7 H1 8R0 sing 24 n n C8 H2 8R0 sing 25 n n C8 H3 8R0 sing 26 n n C10 H4 8R0 sing 27 n n C13 H5 8R0 sing 28 n n C20 H6 8R0 sing 29 n n C12 H7 8R0 sing 30 n n C11 H8 8R0 sing 31 n n C14 H9 8R0 sing 32 n n N17 H10 8R0 sing 33 n n C19 H11 8R0 sing 34 n n C1 H12 8R0 sing 35 n n C2 H13 8R0 sing 36 n n C23 H16 8R0 sing 37 n n C23 H14 8R0 sing 38 n n C23 H15 8R0 sing 39 n n # _atom_sites.entry_id 5Y7T _atom_sites.fract_transf_matrix[1][1] 0.013611 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00843 _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] 0.015054 _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 B 2 FE B 1 401 1 FE FE . C 3 8R0 B 1 402 1 8R0 58K . D 4 AKG B 1 403 1 AKG AKG . E 5 HOH B 1 501 114 HOH HOH . E 5 HOH B 2 502 101 HOH HOH . E 5 HOH B 3 503 9 HOH HOH . E 5 HOH B 4 504 34 HOH HOH . E 5 HOH B 5 505 66 HOH HOH . E 5 HOH B 6 506 3 HOH HOH . E 5 HOH B 7 507 115 HOH HOH . E 5 HOH B 8 508 27 HOH HOH . E 5 HOH B 9 509 55 HOH HOH . E 5 HOH B 10 510 77 HOH HOH . E 5 HOH B 11 511 21 HOH HOH . E 5 HOH B 12 512 10 HOH HOH . E 5 HOH B 13 513 94 HOH HOH . E 5 HOH B 14 514 20 HOH HOH . E 5 HOH B 15 515 59 HOH HOH . E 5 HOH B 16 516 31 HOH HOH . E 5 HOH B 17 517 58 HOH HOH . E 5 HOH B 18 518 4 HOH HOH . E 5 HOH B 19 519 15 HOH HOH . E 5 HOH B 20 520 30 HOH HOH . E 5 HOH B 21 521 57 HOH HOH . E 5 HOH B 22 522 46 HOH HOH . E 5 HOH B 23 523 13 HOH HOH . E 5 HOH B 24 524 25 HOH HOH . E 5 HOH B 25 525 7 HOH HOH . E 5 HOH B 26 526 38 HOH HOH . E 5 HOH B 27 527 71 HOH HOH . E 5 HOH B 28 528 67 HOH HOH . E 5 HOH B 29 529 54 HOH HOH . E 5 HOH B 30 530 74 HOH HOH . E 5 HOH B 31 531 44 HOH HOH . E 5 HOH B 32 532 2 HOH HOH . E 5 HOH B 33 533 53 HOH HOH . E 5 HOH B 34 534 39 HOH HOH . E 5 HOH B 35 535 69 HOH HOH . E 5 HOH B 36 536 110 HOH HOH . E 5 HOH B 37 537 11 HOH HOH . E 5 HOH B 38 538 56 HOH HOH . E 5 HOH B 39 539 49 HOH HOH . E 5 HOH B 40 540 43 HOH HOH . E 5 HOH B 41 541 37 HOH HOH . E 5 HOH B 42 542 36 HOH HOH . E 5 HOH B 43 543 1 HOH HOH . E 5 HOH B 44 544 78 HOH HOH . E 5 HOH B 45 545 89 HOH HOH . E 5 HOH B 46 546 32 HOH HOH . E 5 HOH B 47 547 5 HOH HOH . E 5 HOH B 48 548 45 HOH HOH . E 5 HOH B 49 549 8 HOH HOH . E 5 HOH B 50 550 61 HOH HOH . E 5 HOH B 51 551 95 HOH HOH . E 5 HOH B 52 552 70 HOH HOH . E 5 HOH B 53 553 48 HOH HOH . E 5 HOH B 54 554 23 HOH HOH . E 5 HOH B 55 555 50 HOH HOH . E 5 HOH B 56 556 16 HOH HOH . E 5 HOH B 57 557 76 HOH HOH . E 5 HOH B 58 558 29 HOH HOH . E 5 HOH B 59 559 64 HOH HOH . E 5 HOH B 60 560 33 HOH HOH . E 5 HOH B 61 561 35 HOH HOH . E 5 HOH B 62 562 65 HOH HOH . E 5 HOH B 63 563 41 HOH HOH . E 5 HOH B 64 564 86 HOH HOH . E 5 HOH B 65 565 105 HOH HOH . E 5 HOH B 66 566 52 HOH HOH . E 5 HOH B 67 567 90 HOH HOH . E 5 HOH B 68 568 73 HOH HOH . E 5 HOH B 69 569 47 HOH HOH . E 5 HOH B 70 570 63 HOH HOH . E 5 HOH B 71 571 6 HOH HOH . E 5 HOH B 72 572 109 HOH HOH . E 5 HOH B 73 573 14 HOH HOH . E 5 HOH B 74 574 22 HOH HOH . E 5 HOH B 75 575 97 HOH HOH . E 5 HOH B 76 576 106 HOH HOH . E 5 HOH B 77 577 87 HOH HOH . E 5 HOH B 78 578 79 HOH HOH . E 5 HOH B 79 579 62 HOH HOH . E 5 HOH B 80 580 60 HOH HOH . E 5 HOH B 81 581 81 HOH HOH . E 5 HOH B 82 582 68 HOH HOH . E 5 HOH B 83 583 40 HOH HOH . E 5 HOH B 84 584 96 HOH HOH . E 5 HOH B 85 585 12 HOH HOH . E 5 HOH B 86 586 26 HOH HOH . E 5 HOH B 87 587 99 HOH HOH . E 5 HOH B 88 588 113 HOH HOH . E 5 HOH B 89 589 92 HOH HOH . E 5 HOH B 90 590 91 HOH HOH . E 5 HOH B 91 591 51 HOH HOH . E 5 HOH B 92 592 42 HOH HOH . E 5 HOH B 93 593 17 HOH HOH . E 5 HOH B 94 594 103 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 C C4 8R0 . . . C 3 -24.991 -20.041 -3.694 1 39.15 ? C4 8R0 402 B 1 HETATM 2 C C7 8R0 . . . C 3 -25.387 -22.493 -4.04 1 41.98 ? C7 8R0 402 B 1 HETATM 3 C C8 8R0 . . . C 3 -23.993 -23.271 -3.751 1 46.98 ? C8 8R0 402 B 1 HETATM 4 C C10 8R0 . . . C 3 -22.988 -23.312 -1.535 1 44.73 ? C10 8R0 402 B 1 HETATM 5 C C13 8R0 . . . C 3 -24.509 -25.571 -0.688 1 37.51 ? C13 8R0 402 B 1 HETATM 6 C C15 8R0 . . . C 3 -25.995 -22.399 -5.32 1 34.74 ? C15 8R0 402 B 1 HETATM 7 C C20 8R0 . . . C 3 -22.621 -19.254 -7.24 1 37.54 ? C20 8R0 402 B 1 HETATM 8 C C12 8R0 . . . C 3 -23.502 -24.918 0.258 1 39 ? C12 8R0 402 B 1 HETATM 9 C C11 8R0 . . . C 3 -22.786 -23.892 -0.137 1 40.3 ? C11 8R0 402 B 1 HETATM 10 C C14 8R0 . . . C 3 -24.671 -25.082 -1.904 1 43 ? C14 8R0 402 B 1 HETATM 11 C C9 8R0 . . . C 3 -23.861 -23.863 -2.354 1 45.7 ? C9 8R0 402 B 1 HETATM 12 O O16 8R0 . . . C 3 -26.864 -23.118 -5.652 1 30.94 ? O16 8R0 402 B 1 HETATM 13 N N17 8R0 . . . C 3 -25.544 -21.411 -6.212 1 35.07 ? N17 8R0 402 B 1 HETATM 14 C C18 8R0 . . . C 3 -24.509 -20.454 -6.097 1 37.51 ? C18 8R0 402 B 1 HETATM 15 C C19 8R0 . . . C 3 -23.718 -20.147 -7.202 1 31.44 ? C19 8R0 402 B 1 HETATM 16 C C1 8R0 . . . C 3 -22.337 -18.591 -6.005 1 41.78 ? C1 8R0 402 B 1 HETATM 17 C C2 8R0 . . . C 3 -23.111 -18.828 -4.873 1 38.51 ? C2 8R0 402 B 1 HETATM 18 C C3 8R0 . . . C 3 -24.249 -19.803 -4.864 1 38.48 ? C3 8R0 402 B 1 HETATM 19 O O5 8R0 . . . C 3 -25.147 -19.074 -3.016 1 31.55 ? O5 8R0 402 B 1 HETATM 20 N N6 8R0 . . . C 3 -25.548 -21.246 -3.231 1 44.3 ? N6 8R0 402 B 1 HETATM 21 C C23 8R0 . . . C 3 -26.278 -21.332 -1.977 1 46.68 ? C23 8R0 402 B 1 HETATM 22 H H1 8R0 . . . C 3 -26.023 -22.922 -3.498 1 50.38 ? H1 8R0 402 B 1 HETATM 23 H H2 8R0 . . . C 3 -23.286 -22.668 -3.884 1 56.37 ? H2 8R0 402 B 1 HETATM 24 H H3 8R0 . . . C 3 -23.909 -23.968 -4.376 1 56.37 ? H3 8R0 402 B 1 HETATM 25 H H4 8R0 . . . C 3 -22.483 -22.582 -1.815 1 53.68 ? H4 8R0 402 B 1 HETATM 26 H H5 8R0 . . . C 3 -25.007 -26.304 -0.408 1 45.01 ? H5 8R0 402 B 1 HETATM 27 H H6 8R0 . . . C 3 -22.133 -19.096 -8.014 1 45.05 ? H6 8R0 402 B 1 HETATM 28 H H7 8R0 . . . C 3 -23.382 -25.263 1.113 1 46.8 ? H7 8R0 402 B 1 HETATM 29 H H8 8R0 . . . C 3 -22.181 -23.495 0.447 1 48.36 ? H8 8R0 402 B 1 HETATM 30 H H9 8R0 . . . C 3 -25.286 -25.47 -2.483 1 51.61 ? H9 8R0 402 B 1 HETATM 31 H H10 8R0 . . . C 3 -25.946 -21.414 -6.982 1 42.09 ? H10 8R0 402 B 1 HETATM 32 H H11 8R0 . . . C 3 -23.89 -20.572 -7.925 1 37.73 ? H11 8R0 402 B 1 HETATM 33 H H12 8R0 . . . C 3 -21.65 -17.967 -5.968 1 50.14 ? H12 8R0 402 B 1 HETATM 34 H H13 8R0 . . . C 3 -22.915 -18.418 -4.148 1 46.21 ? H13 8R0 402 B 1 HETATM 35 H H16 8R0 . . . C 3 -25.909 -22.013 -1.446 1 56.02 ? H16 8R0 402 B 1 HETATM 36 H H14 8R0 . . . C 3 -27.18 -21.526 -2.152 1 56.02 ? H14 8R0 402 B 1 HETATM 37 H H15 8R0 . . . C 3 -26.217 -20.512 -1.522 1 56.02 ? H15 8R0 402 B 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 313 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 37 #