data_7JR5 # _model_server_result.job_id qntB3vvxDqkDz_u7Z2e_pg _model_server_result.datetime_utc '2025-01-19 00:18:11' _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 7jr5 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":601}' # _entry.id 7JR5 # _exptl.entry_id 7JR5 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 120.152 _entity.id 3 _entity.src_method nat _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 107.63 _cell.angle_gamma 90 _cell.entry_id 7JR5 _cell.length_a 83.69 _cell.length_b 83.4 _cell.length_c 86.87 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7JR5 _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _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 _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 D _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 covale ? covale1 A SG CYS 13 A CYS 13 1_555 C CBC VHG . A VHG 500 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.851 ? covale ? covale2 A SG CYS 13 A CYS 13 1_555 C CBC VHG . A VHG 500 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.851 ? covale ? covale3 B SG CYS 13 B CYS 13 1_555 E CBC VHG . B VHG 602 1_555 ? A ? ? A ? ? ? ? ? ? ? 1.851 ? covale ? covale4 B SG CYS 13 B CYS 13 1_555 E CBC VHG . B VHG 602 1_555 ? B ? ? B ? ? ? ? ? ? ? 1.852 ? # _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 7JR5 _atom_sites.fract_transf_matrix[1][1] 0.011949 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.003797 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01199 _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] 0.012079 _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 VHG A 1 500 500 VHG EL5 . D 3 BEN B 1 601 601 BEN BEN . E 2 VHG B 1 602 500 VHG EL5 . F 4 HOH A 1 601 32 HOH HOH . F 4 HOH A 2 602 72 HOH HOH . F 4 HOH A 3 603 37 HOH HOH . F 4 HOH A 4 604 103 HOH HOH . F 4 HOH A 5 605 61 HOH HOH . F 4 HOH A 6 606 7 HOH HOH . F 4 HOH A 7 607 28 HOH HOH . F 4 HOH A 8 608 105 HOH HOH . F 4 HOH A 9 609 25 HOH HOH . F 4 HOH A 10 610 97 HOH HOH . F 4 HOH A 11 611 65 HOH HOH . F 4 HOH A 12 612 2 HOH HOH . F 4 HOH A 13 613 73 HOH HOH . F 4 HOH A 14 614 58 HOH HOH . F 4 HOH A 15 615 1 HOH HOH . F 4 HOH A 16 616 33 HOH HOH . F 4 HOH A 17 617 117 HOH HOH . F 4 HOH A 18 618 35 HOH HOH . F 4 HOH A 19 619 112 HOH HOH . F 4 HOH A 20 620 14 HOH HOH . F 4 HOH A 21 621 98 HOH HOH . F 4 HOH A 22 622 22 HOH HOH . F 4 HOH A 23 623 116 HOH HOH . F 4 HOH A 24 624 127 HOH HOH . F 4 HOH A 25 625 94 HOH HOH . F 4 HOH A 26 626 46 HOH HOH . F 4 HOH A 27 627 95 HOH HOH . F 4 HOH A 28 628 19 HOH HOH . F 4 HOH A 29 629 23 HOH HOH . F 4 HOH A 30 630 15 HOH HOH . F 4 HOH A 31 631 29 HOH HOH . F 4 HOH A 32 632 92 HOH HOH . F 4 HOH A 33 633 118 HOH HOH . F 4 HOH A 34 634 81 HOH HOH . F 4 HOH A 35 635 39 HOH HOH . F 4 HOH A 36 636 8 HOH HOH . F 4 HOH A 37 637 62 HOH HOH . F 4 HOH A 38 638 75 HOH HOH . F 4 HOH A 39 639 42 HOH HOH . F 4 HOH A 40 640 88 HOH HOH . F 4 HOH A 41 641 119 HOH HOH . F 4 HOH A 42 642 102 HOH HOH . F 4 HOH A 43 643 21 HOH HOH . F 4 HOH A 44 644 106 HOH HOH . F 4 HOH A 45 645 36 HOH HOH . F 4 HOH A 46 646 101 HOH HOH . F 4 HOH A 47 647 113 HOH HOH . F 4 HOH A 48 648 107 HOH HOH . F 4 HOH A 49 649 86 HOH HOH . F 4 HOH A 50 650 38 HOH HOH . F 4 HOH A 51 651 57 HOH HOH . F 4 HOH A 52 652 30 HOH HOH . F 4 HOH A 53 653 40 HOH HOH . F 4 HOH A 54 654 83 HOH HOH . F 4 HOH A 55 655 89 HOH HOH . G 4 HOH B 1 701 55 HOH HOH . G 4 HOH B 2 702 84 HOH HOH . G 4 HOH B 3 703 34 HOH HOH . G 4 HOH B 4 704 109 HOH HOH . G 4 HOH B 5 705 16 HOH HOH . G 4 HOH B 6 706 130 HOH HOH . G 4 HOH B 7 707 79 HOH HOH . G 4 HOH B 8 708 104 HOH HOH . G 4 HOH B 9 709 12 HOH HOH . G 4 HOH B 10 710 70 HOH HOH . G 4 HOH B 11 711 85 HOH HOH . G 4 HOH B 12 712 17 HOH HOH . G 4 HOH B 13 713 3 HOH HOH . G 4 HOH B 14 714 50 HOH HOH . G 4 HOH B 15 715 51 HOH HOH . G 4 HOH B 16 716 78 HOH HOH . G 4 HOH B 17 717 45 HOH HOH . G 4 HOH B 18 718 108 HOH HOH . G 4 HOH B 19 719 10 HOH HOH . G 4 HOH B 20 720 114 HOH HOH . G 4 HOH B 21 721 49 HOH HOH . G 4 HOH B 22 722 74 HOH HOH . G 4 HOH B 23 723 91 HOH HOH . G 4 HOH B 24 724 59 HOH HOH . G 4 HOH B 25 725 87 HOH HOH . G 4 HOH B 26 726 111 HOH HOH . G 4 HOH B 27 727 121 HOH HOH . G 4 HOH B 28 728 120 HOH HOH . G 4 HOH B 29 729 71 HOH HOH . G 4 HOH B 30 730 52 HOH HOH . G 4 HOH B 31 731 100 HOH HOH . G 4 HOH B 32 732 47 HOH HOH . G 4 HOH B 33 733 53 HOH HOH . G 4 HOH B 34 734 56 HOH HOH . G 4 HOH B 35 735 69 HOH HOH . G 4 HOH B 36 736 77 HOH HOH . G 4 HOH B 37 737 93 HOH HOH . G 4 HOH B 38 738 90 HOH HOH . G 4 HOH B 39 739 76 HOH HOH . G 4 HOH B 40 740 99 HOH HOH . G 4 HOH B 41 741 43 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 . . . D 3 -54.197 -17.249 -27.224 1 72.26 ? C1 BEN 601 B 1 HETATM 2 C C2 BEN . . . D 3 -54.763 -16.391 -26.291 1 72.69 ? C2 BEN 601 B 1 HETATM 3 C C3 BEN . . . D 3 -56.132 -16.389 -26.087 1 77.84 ? C3 BEN 601 B 1 HETATM 4 C C4 BEN . . . D 3 -56.942 -17.23 -26.812 1 77.78 ? C4 BEN 601 B 1 HETATM 5 C C5 BEN . . . D 3 -56.393 -18.076 -27.746 1 73.58 ? C5 BEN 601 B 1 HETATM 6 C C6 BEN . . . D 3 -55.027 -18.09 -27.954 1 72.74 ? C6 BEN 601 B 1 HETATM 7 C C BEN . . . D 3 -52.729 -17.256 -27.457 1 75.18 ? C BEN 601 B 1 HETATM 8 N N1 BEN . . . D 3 -52.055 -18.345 -27.637 1 70.69 ? N1 BEN 601 B 1 HETATM 9 N N2 BEN . . . D 3 -52.098 -16.063 -27.482 1 80.33 ? N2 BEN 601 B 1 # _model_server_stats.io_time_ms 21 _model_server_stats.parse_time_ms 17 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 364 _model_server_stats.encode_time_ms 19 _model_server_stats.element_count 9 #