data_6XEF # _model_server_result.job_id IxSBR_VKLhYZPZMyARnmCQ _model_server_result.datetime_utc '2024-11-25 23:56:56' _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 6xef # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 6XEF # _exptl.entry_id 6XEF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 120.152 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description BENZAMIDINE _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 120 _cell.entry_id 6XEF _cell.length_a 88.384 _cell.length_b 88.384 _cell.length_c 104.879 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6XEF _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 1' # _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,F,G _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 5 _struct_asym.id F _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 O PRO 89 A PRO 89 1_555 C MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.511 ? metalc ? metalc2 A OD1 ASN 90 A ASN 90 1_555 D MG MG . A MG 403 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.574 ? metalc ? metalc3 D MG MG . A MG 403 1_555 G O HOH . A HOH 622 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.78 ? # _chem_comp.formula 'C7 H8 N2' _chem_comp.formula_weight 120.152 _chem_comp.id BEN _chem_comp.mon_nstd_flag . _chem_comp.name BENZAMIDINE _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 C1 C2 BEN doub 70 n y C1 C6 BEN sing 71 n y C1 C BEN sing 72 n n C2 C3 BEN sing 73 n y C2 H2 BEN sing 74 n n C3 C4 BEN doub 75 n y C3 H3 BEN sing 76 n n C4 C5 BEN sing 77 n y C4 H4 BEN sing 78 n n C5 C6 BEN doub 79 n y C5 H5 BEN sing 80 n n C6 H6 BEN sing 81 n n C N1 BEN doub 82 e n C N2 BEN sing 83 n n N1 HN1 BEN sing 84 n n N2 HN21 BEN sing 85 n n N2 HN22 BEN sing 86 n n # _atom_sites.entry_id 6XEF _atom_sites.fract_transf_matrix[1][1] 0.011314 _atom_sites.fract_transf_matrix[1][2] 0.006532 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.013065 _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] 0.009535 _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 TRS A 1 401 1 TRS TRS . C 3 MG A 1 402 2 MG MG . D 3 MG A 1 403 3 MG MG . E 4 VO4 A 1 404 4 VO4 VO4 . F 5 BEN A 1 405 5 BEN BEN . G 6 HOH A 1 501 49 HOH HOH . G 6 HOH A 2 502 123 HOH HOH . G 6 HOH A 3 503 28 HOH HOH . G 6 HOH A 4 504 44 HOH HOH . G 6 HOH A 5 505 86 HOH HOH . G 6 HOH A 6 506 85 HOH HOH . G 6 HOH A 7 507 57 HOH HOH . G 6 HOH A 8 508 117 HOH HOH . G 6 HOH A 9 509 99 HOH HOH . G 6 HOH A 10 510 77 HOH HOH . G 6 HOH A 11 511 50 HOH HOH . G 6 HOH A 12 512 36 HOH HOH . G 6 HOH A 13 513 71 HOH HOH . G 6 HOH A 14 514 79 HOH HOH . G 6 HOH A 15 515 131 HOH HOH . G 6 HOH A 16 516 76 HOH HOH . G 6 HOH A 17 517 3 HOH HOH . G 6 HOH A 18 518 111 HOH HOH . G 6 HOH A 19 519 75 HOH HOH . G 6 HOH A 20 520 48 HOH HOH . G 6 HOH A 21 521 135 HOH HOH . G 6 HOH A 22 522 12 HOH HOH . G 6 HOH A 23 523 22 HOH HOH . G 6 HOH A 24 524 130 HOH HOH . G 6 HOH A 25 525 70 HOH HOH . G 6 HOH A 26 526 93 HOH HOH . G 6 HOH A 27 527 136 HOH HOH . G 6 HOH A 28 528 119 HOH HOH . G 6 HOH A 29 529 20 HOH HOH . G 6 HOH A 30 530 63 HOH HOH . G 6 HOH A 31 531 116 HOH HOH . G 6 HOH A 32 532 19 HOH HOH . G 6 HOH A 33 533 13 HOH HOH . G 6 HOH A 34 534 41 HOH HOH . G 6 HOH A 35 535 6 HOH HOH . G 6 HOH A 36 536 64 HOH HOH . G 6 HOH A 37 537 72 HOH HOH . G 6 HOH A 38 538 52 HOH HOH . G 6 HOH A 39 539 67 HOH HOH . G 6 HOH A 40 540 59 HOH HOH . G 6 HOH A 41 541 54 HOH HOH . G 6 HOH A 42 542 98 HOH HOH . G 6 HOH A 43 543 34 HOH HOH . G 6 HOH A 44 544 8 HOH HOH . G 6 HOH A 45 545 97 HOH HOH . G 6 HOH A 46 546 133 HOH HOH . G 6 HOH A 47 547 5 HOH HOH . G 6 HOH A 48 548 101 HOH HOH . G 6 HOH A 49 549 23 HOH HOH . G 6 HOH A 50 550 107 HOH HOH . G 6 HOH A 51 551 80 HOH HOH . G 6 HOH A 52 552 95 HOH HOH . G 6 HOH A 53 553 11 HOH HOH . G 6 HOH A 54 554 58 HOH HOH . G 6 HOH A 55 555 4 HOH HOH . G 6 HOH A 56 556 96 HOH HOH . G 6 HOH A 57 557 16 HOH HOH . G 6 HOH A 58 558 88 HOH HOH . G 6 HOH A 59 559 14 HOH HOH . G 6 HOH A 60 560 27 HOH HOH . G 6 HOH A 61 561 90 HOH HOH . G 6 HOH A 62 562 104 HOH HOH . G 6 HOH A 63 563 89 HOH HOH . G 6 HOH A 64 564 15 HOH HOH . G 6 HOH A 65 565 82 HOH HOH . G 6 HOH A 66 566 39 HOH HOH . G 6 HOH A 67 567 42 HOH HOH . G 6 HOH A 68 568 2 HOH HOH . G 6 HOH A 69 569 84 HOH HOH . G 6 HOH A 70 570 47 HOH HOH . G 6 HOH A 71 571 55 HOH HOH . G 6 HOH A 72 572 10 HOH HOH . G 6 HOH A 73 573 31 HOH HOH . G 6 HOH A 74 574 40 HOH HOH . G 6 HOH A 75 575 35 HOH HOH . G 6 HOH A 76 576 68 HOH HOH . G 6 HOH A 77 577 134 HOH HOH . G 6 HOH A 78 578 78 HOH HOH . G 6 HOH A 79 579 112 HOH HOH . G 6 HOH A 80 580 122 HOH HOH . G 6 HOH A 81 581 121 HOH HOH . G 6 HOH A 82 582 1 HOH HOH . G 6 HOH A 83 583 118 HOH HOH . G 6 HOH A 84 584 100 HOH HOH . G 6 HOH A 85 585 24 HOH HOH . G 6 HOH A 86 586 74 HOH HOH . G 6 HOH A 87 587 46 HOH HOH . G 6 HOH A 88 588 60 HOH HOH . G 6 HOH A 89 589 33 HOH HOH . G 6 HOH A 90 590 29 HOH HOH . G 6 HOH A 91 591 26 HOH HOH . G 6 HOH A 92 592 128 HOH HOH . G 6 HOH A 93 593 21 HOH HOH . G 6 HOH A 94 594 7 HOH HOH . G 6 HOH A 95 595 38 HOH HOH . G 6 HOH A 96 596 81 HOH HOH . G 6 HOH A 97 597 43 HOH HOH . G 6 HOH A 98 598 56 HOH HOH . G 6 HOH A 99 599 132 HOH HOH . G 6 HOH A 100 600 51 HOH HOH . G 6 HOH A 101 601 114 HOH HOH . G 6 HOH A 102 602 62 HOH HOH . G 6 HOH A 103 603 69 HOH HOH . G 6 HOH A 104 604 17 HOH HOH . G 6 HOH A 105 605 66 HOH HOH . G 6 HOH A 106 606 30 HOH HOH . G 6 HOH A 107 607 32 HOH HOH . G 6 HOH A 108 608 102 HOH HOH . G 6 HOH A 109 609 18 HOH HOH . G 6 HOH A 110 610 94 HOH HOH . G 6 HOH A 111 611 106 HOH HOH . G 6 HOH A 112 612 110 HOH HOH . G 6 HOH A 113 613 45 HOH HOH . G 6 HOH A 114 614 25 HOH HOH . G 6 HOH A 115 615 137 HOH HOH . G 6 HOH A 116 616 113 HOH HOH . G 6 HOH A 117 617 124 HOH HOH . G 6 HOH A 118 618 126 HOH HOH . G 6 HOH A 119 619 92 HOH HOH . G 6 HOH A 120 620 115 HOH HOH . G 6 HOH A 121 621 91 HOH HOH . G 6 HOH A 122 622 103 HOH HOH . G 6 HOH A 123 623 127 HOH HOH . G 6 HOH A 124 624 73 HOH HOH . G 6 HOH A 125 625 53 HOH HOH . G 6 HOH A 126 626 83 HOH HOH . G 6 HOH A 127 627 108 HOH HOH . G 6 HOH A 128 628 87 HOH HOH . G 6 HOH A 129 629 61 HOH HOH . G 6 HOH A 130 630 105 HOH HOH . G 6 HOH A 131 631 65 HOH HOH . G 6 HOH A 132 632 109 HOH HOH . G 6 HOH A 133 633 129 HOH HOH . G 6 HOH A 134 634 120 HOH HOH . G 6 HOH A 135 635 9 HOH HOH . G 6 HOH A 136 636 37 HOH HOH . G 6 HOH A 137 637 125 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 C C1 BEN . . . F 5 -65.006 18.365 8.708 0.86 66.67 ? C1 BEN 405 A 1 HETATM 2 C C2 BEN . . . F 5 -64.75 17.389 7.758 0.86 67.26 ? C2 BEN 405 A 1 HETATM 3 C C3 BEN . . . F 5 -63.577 17.429 7.022 0.86 67.45 ? C3 BEN 405 A 1 HETATM 4 C C4 BEN . . . F 5 -62.659 18.444 7.238 0.86 67.29 ? C4 BEN 405 A 1 HETATM 5 C C5 BEN . . . F 5 -62.911 19.421 8.189 0.86 65.56 ? C5 BEN 405 A 1 HETATM 6 C C6 BEN . . . F 5 -64.084 19.38 8.926 0.86 65.67 ? C6 BEN 405 A 1 HETATM 7 C C BEN . . . F 5 -66.305 18.318 9.514 0.86 67.19 ? C BEN 405 A 1 HETATM 8 N N1 BEN . . . F 5 -66.787 17.211 9.861 0.86 67.53 ? N1 BEN 405 A 1 HETATM 9 N N2 BEN . . . F 5 -66.977 19.558 9.867 0.86 67.94 ? N2 BEN 405 A 1 # _model_server_stats.io_time_ms 23 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 324 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 9 #