data_6G9B # _model_server_result.job_id Xr7MO1qm1ZuI4mi2I_O6Uw _model_server_result.datetime_utc '2024-11-24 08:20:54' _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 6g9b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"L","auth_seq_id":609}' # _entry.id 6G9B # _exptl.entry_id 6G9B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 280.407 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 3-(5H-DIBENZO[B,F]AZEPIN-5-YL)-N,N-DIMETHYLPROPAN-1-AMINE _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 6G9B _cell.length_a 114.216 _cell.length_b 114.216 _cell.length_c 305.552 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6G9B _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details hexameric _pdbx_struct_assembly.oligomeric_count 6 _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,K,L,M,N,O,P,Q,R,S,T _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_565 -y,x-y+1,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 -57.108 98.913958 0 3 'crystal symmetry operation' 3_455 -x+y-1,-x,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -114.216 0 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 6 L N N ? 6 Q N N # _pdbx_entity_branch.entity_id 3 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 3 _pdbx_entity_branch_link.entity_branch_list_num_1 2 _pdbx_entity_branch_link.entity_branch_list_num_2 1 _pdbx_entity_branch_link.comp_id_1 NAG _pdbx_entity_branch_link.comp_id_2 NAG _pdbx_entity_branch_link.atom_id_1 C1 _pdbx_entity_branch_link.leaving_atom_id_1 O1 _pdbx_entity_branch_link.atom_stereo_config_1 . _pdbx_entity_branch_link.atom_id_2 O4 _pdbx_entity_branch_link.leaving_atom_id_2 HO4 _pdbx_entity_branch_link.atom_stereo_config_2 . _pdbx_entity_branch_link.value_order sing # loop_ _pdbx_branch_scheme.entity_id _pdbx_branch_scheme.hetero _pdbx_branch_scheme.asym_id _pdbx_branch_scheme.mon_id _pdbx_branch_scheme.num _pdbx_branch_scheme.pdb_asym_id _pdbx_branch_scheme.pdb_seq_num _pdbx_branch_scheme.pdb_mon_id _pdbx_branch_scheme.auth_asym_id _pdbx_branch_scheme.auth_seq_num _pdbx_branch_scheme.auth_mon_id 3 n C NAG 1 C 1 NAG D 621 NAG 3 n C NAG 2 C 2 NAG N 16 NAG # 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 disulf ? disulf1 A SG CYS 26 A CYS 53 1_555 B SG CYS 108 B CYS 609 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.039 ? disulf ? disulf2 A SG CYS 81 A CYS 108 1_555 A SG CYS 108 A CYS 135 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? disulf ? disulf3 A SG CYS 94 A CYS 121 1_555 A SG CYS 120 A CYS 147 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 B SG CYS 10 B CYS 511 1_555 B SG CYS 55 B CYS 556 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf5 B SG CYS 100 B CYS 601 1_555 B SG CYS 107 B CYS 608 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? covale ? covale1 A ND2 ASN 201 A ASN 228 1_555 F C1 NAG . A NAG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.454 ? covale ? covale2 A ND2 ASN 211 A ASN 238 1_555 E C1 NAG . A NAG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale3 A ND2 ASN 230 A ASN 257 1_555 D C1 NAG . A NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale4 A ND2 ASN 241 A ASN 268 1_555 G C1 NAG . A NAG 604 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 B ND2 ASN 62 B ASN 563 1_555 C C1 NAG . C NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.43 ? covale ? covale6 C O4 NAG . C NAG 1 1_555 C C1 NAG . C NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? # _chem_comp.formula 'C19 H24 N2' _chem_comp.formula_weight 280.407 _chem_comp.id IXX _chem_comp.mon_nstd_flag . _chem_comp.name 3-(5H-DIBENZO[B,F]AZEPIN-5-YL)-N,N-DIMETHYLPROPAN-1-AMINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 5-(3-(dimethylamino)propyl)-10,11-dihydro-5H-dibenz[b,f]azepine;10,11-Dehydroimipramine;Depramine # 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 C11 N1 IXX sing 195 n n C11 C10 IXX doub 196 n y C11 C12 IXX sing 197 n y C10 C9 IXX sing 198 n y C10 H10 IXX sing 199 n n C9 C8 IXX doub 200 n y C9 H9 IXX sing 201 n n C8 C7 IXX sing 202 n y C8 H8 IXX sing 203 n n C7 C12 IXX doub 204 n y C7 H7 IXX sing 205 n n C2 C1 IXX sing 206 n y C2 C3 IXX doub 207 n y C2 H2 IXX sing 208 n n C6 C12 IXX sing 209 n n C6 C5 IXX sing 210 n n C6 H61 IXX sing 211 n n C5 C13 IXX sing 212 n n C5 H51 IXX sing 213 n n N1 C15 IXX sing 214 n n N1 C14 IXX sing 215 n n C3 C4 IXX sing 216 n y C3 H3 IXX sing 217 n n N2 C19 IXX sing 218 n n N2 C18 IXX sing 219 n n N2 C17 IXX sing 220 n n C4 C13 IXX doub 221 n y C4 H4 IXX sing 222 n n C1 C14 IXX doub 223 n y C1 H1 IXX sing 224 n n C13 C14 IXX sing 225 n y C15 C16 IXX sing 226 n n C15 H151 IXX sing 227 n n C15 H152 IXX sing 228 n n C16 C17 IXX sing 229 n n C16 H161 IXX sing 230 n n C16 H162 IXX sing 231 n n C17 H171 IXX sing 232 n n C17 H172 IXX sing 233 n n C18 H181 IXX sing 234 n n C18 H182 IXX sing 235 n n C18 H183 IXX sing 236 n n C19 H191 IXX sing 237 n n C19 H192 IXX sing 238 n n C19 H193 IXX sing 239 n n C5 H52 IXX sing 240 n n C6 H62 IXX sing 241 n n # _atom_sites.entry_id 6G9B _atom_sites.fract_transf_matrix[1][1] 0.008755 _atom_sites.fract_transf_matrix[1][2] 0.005055 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01011 _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] 0.003273 _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 D 4 NAG A 1 601 2 NAG NAG . E 4 NAG A 1 602 11 NAG NAG . F 4 NAG A 1 603 14 NAG NAG . G 4 NAG A 1 604 15 NAG NAG . H 5 GOL A 1 605 1 GOL GOL . I 5 GOL A 1 606 2 GOL GOL . J 5 GOL A 1 607 5 GOL GOL . K 5 GOL A 1 608 6 GOL GOL . L 6 IXX A 1 609 1 IXX IXX . M 7 DMS A 1 610 2 DMS DMS . N 7 DMS A 1 611 3 DMS DMS . O 5 GOL B 1 703 3 GOL GOL . P 5 GOL B 1 704 4 GOL GOL . Q 6 IXX B 1 705 2 IXX IXX . R 7 DMS B 1 706 1 DMS DMS . S 8 HOH A 1 701 51 HOH HOH . S 8 HOH A 2 702 62 HOH HOH . S 8 HOH A 3 703 120 HOH HOH . S 8 HOH A 4 704 133 HOH HOH . S 8 HOH A 5 705 118 HOH HOH . S 8 HOH A 6 706 58 HOH HOH . S 8 HOH A 7 707 4 HOH HOH . S 8 HOH A 8 708 50 HOH HOH . S 8 HOH A 9 709 12 HOH HOH . S 8 HOH A 10 710 76 HOH HOH . S 8 HOH A 11 711 38 HOH HOH . S 8 HOH A 12 712 18 HOH HOH . S 8 HOH A 13 713 20 HOH HOH . S 8 HOH A 14 714 61 HOH HOH . S 8 HOH A 15 715 73 HOH HOH . S 8 HOH A 16 716 7 HOH HOH . S 8 HOH A 17 717 11 HOH HOH . S 8 HOH A 18 718 1 HOH HOH . S 8 HOH A 19 719 115 HOH HOH . S 8 HOH A 20 720 6 HOH HOH . S 8 HOH A 21 721 41 HOH HOH . S 8 HOH A 22 722 119 HOH HOH . S 8 HOH A 23 723 5 HOH HOH . S 8 HOH A 24 724 113 HOH HOH . S 8 HOH A 25 725 146 HOH HOH . S 8 HOH A 26 726 40 HOH HOH . S 8 HOH A 27 727 17 HOH HOH . S 8 HOH A 28 728 37 HOH HOH . S 8 HOH A 29 729 8 HOH HOH . S 8 HOH A 30 730 25 HOH HOH . S 8 HOH A 31 731 2 HOH HOH . S 8 HOH A 32 732 9 HOH HOH . S 8 HOH A 33 733 10 HOH HOH . S 8 HOH A 34 734 69 HOH HOH . S 8 HOH A 35 735 31 HOH HOH . S 8 HOH A 36 736 100 HOH HOH . S 8 HOH A 37 737 56 HOH HOH . S 8 HOH A 38 738 135 HOH HOH . S 8 HOH A 39 739 54 HOH HOH . S 8 HOH A 40 740 85 HOH HOH . S 8 HOH A 41 741 80 HOH HOH . S 8 HOH A 42 742 14 HOH HOH . S 8 HOH A 43 743 134 HOH HOH . S 8 HOH A 44 744 34 HOH HOH . S 8 HOH A 45 745 79 HOH HOH . S 8 HOH A 46 746 68 HOH HOH . S 8 HOH A 47 747 88 HOH HOH . S 8 HOH A 48 748 23 HOH HOH . S 8 HOH A 49 749 33 HOH HOH . S 8 HOH A 50 750 84 HOH HOH . S 8 HOH A 51 751 26 HOH HOH . S 8 HOH A 52 752 15 HOH HOH . S 8 HOH A 53 753 152 HOH HOH . S 8 HOH A 54 754 148 HOH HOH . S 8 HOH A 55 755 97 HOH HOH . S 8 HOH A 56 756 72 HOH HOH . S 8 HOH A 57 757 121 HOH HOH . S 8 HOH A 58 758 151 HOH HOH . S 8 HOH A 59 759 125 HOH HOH . S 8 HOH A 60 760 156 HOH HOH . S 8 HOH A 61 761 141 HOH HOH . S 8 HOH A 62 762 102 HOH HOH . S 8 HOH A 63 763 46 HOH HOH . S 8 HOH A 64 764 114 HOH HOH . S 8 HOH A 65 765 83 HOH HOH . S 8 HOH A 66 766 22 HOH HOH . S 8 HOH A 67 767 155 HOH HOH . S 8 HOH A 68 768 145 HOH HOH . S 8 HOH A 69 769 153 HOH HOH . S 8 HOH A 70 770 105 HOH HOH . S 8 HOH A 71 771 144 HOH HOH . S 8 HOH A 72 772 154 HOH HOH . S 8 HOH A 73 773 123 HOH HOH . S 8 HOH A 74 774 42 HOH HOH . S 8 HOH A 75 775 142 HOH HOH . S 8 HOH A 76 776 158 HOH HOH . S 8 HOH A 77 777 157 HOH HOH . S 8 HOH A 78 778 160 HOH HOH . S 8 HOH A 79 779 159 HOH HOH . S 8 HOH A 80 780 53 HOH HOH . S 8 HOH A 81 781 28 HOH HOH . S 8 HOH A 82 782 111 HOH HOH . T 8 HOH B 1 801 77 HOH HOH . T 8 HOH B 2 802 67 HOH HOH . T 8 HOH B 3 803 71 HOH HOH . T 8 HOH B 4 804 96 HOH HOH . T 8 HOH B 5 805 16 HOH HOH . T 8 HOH B 6 806 64 HOH HOH . T 8 HOH B 7 807 19 HOH HOH . T 8 HOH B 8 808 3 HOH HOH . T 8 HOH B 9 809 52 HOH HOH . T 8 HOH B 10 810 63 HOH HOH . T 8 HOH B 11 811 24 HOH HOH . T 8 HOH B 12 812 59 HOH HOH . T 8 HOH B 13 813 21 HOH HOH . T 8 HOH B 14 814 29 HOH HOH . T 8 HOH B 15 815 55 HOH HOH . T 8 HOH B 16 816 32 HOH HOH . T 8 HOH B 17 817 47 HOH HOH . T 8 HOH B 18 818 49 HOH HOH . T 8 HOH B 19 819 150 HOH HOH . T 8 HOH B 20 820 106 HOH HOH . T 8 HOH B 21 821 57 HOH HOH . T 8 HOH B 22 822 44 HOH HOH . T 8 HOH B 23 823 13 HOH HOH . T 8 HOH B 24 824 143 HOH HOH . T 8 HOH B 25 825 149 HOH HOH . T 8 HOH B 26 826 35 HOH HOH . T 8 HOH B 27 827 110 HOH HOH . T 8 HOH B 28 828 108 HOH HOH . T 8 HOH B 29 829 81 HOH HOH . T 8 HOH B 30 830 27 HOH HOH . T 8 HOH B 31 831 60 HOH HOH . T 8 HOH B 32 832 112 HOH HOH . T 8 HOH B 33 833 138 HOH HOH . T 8 HOH B 34 834 36 HOH HOH . T 8 HOH B 35 835 99 HOH HOH . T 8 HOH B 36 836 161 HOH HOH . T 8 HOH B 37 837 65 HOH HOH . T 8 HOH B 38 838 140 HOH HOH . T 8 HOH B 39 839 162 HOH HOH . T 8 HOH B 40 840 137 HOH HOH . T 8 HOH B 41 841 139 HOH HOH . T 8 HOH B 42 842 43 HOH HOH . T 8 HOH B 43 843 130 HOH HOH . T 8 HOH B 44 844 45 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 C11 IXX . . . L 6 -48.776 11.545 -2.859 1 83.31 ? C11 IXX 609 A 1 HETATM 2 C C10 IXX . . . L 6 -49.112 12.474 -1.87 1 83.9 ? C10 IXX 609 A 1 HETATM 3 C C9 IXX . . . L 6 -50.427 12.565 -1.403 1 82.4 ? C9 IXX 609 A 1 HETATM 4 C C8 IXX . . . L 6 -51.405 11.734 -1.91 1 84.66 ? C8 IXX 609 A 1 HETATM 5 C C7 IXX . . . L 6 -51.083 10.801 -2.893 1 83.83 ? C7 IXX 609 A 1 HETATM 6 C C2 IXX . . . L 6 -46.876 13.507 -6.62 1 88.04 ? C2 IXX 609 A 1 HETATM 7 C C6 IXX . . . L 6 -49.442 9.655 -4.472 1 84.23 ? C6 IXX 609 A 1 HETATM 8 C C5 IXX . . . L 6 -48.016 9.664 -5.037 1 86.12 ? C5 IXX 609 A 1 HETATM 9 N N1 IXX . . . L 6 -47.41 11.34 -3.442 1 86.41 ? N1 IXX 609 A 1 HETATM 10 C C3 IXX . . . L 6 -47.235 12.532 -7.563 1 88.38 ? C3 IXX 609 A 1 HETATM 11 N N2 IXX . . . L 6 -44.331 9.855 0.059 1 113.2 ? N2 IXX 609 A 1 HETATM 12 C C4 IXX . . . L 6 -47.617 11.264 -7.133 1 87.44 ? C4 IXX 609 A 1 HETATM 13 C C1 IXX . . . L 6 -46.9 13.205 -5.245 1 88.11 ? C1 IXX 609 A 1 HETATM 14 C C12 IXX . . . L 6 -49.765 10.709 -3.355 1 82.96 ? C12 IXX 609 A 1 HETATM 15 C C13 IXX . . . L 6 -47.649 10.962 -5.74 1 86.72 ? C13 IXX 609 A 1 HETATM 16 C C14 IXX . . . L 6 -47.291 11.919 -4.817 1 85.73 ? C14 IXX 609 A 1 HETATM 17 C C15 IXX . . . L 6 -46.4 11.864 -2.546 1 93.92 ? C15 IXX 609 A 1 HETATM 18 C C16 IXX . . . L 6 -45.99 10.689 -1.573 1 98.81 ? C16 IXX 609 A 1 HETATM 19 C C17 IXX . . . L 6 -44.677 11.029 -0.835 1 107.17 ? C17 IXX 609 A 1 HETATM 20 C C18 IXX . . . L 6 -43.387 8.989 -0.629 1 113.7 ? C18 IXX 609 A 1 HETATM 21 C C19 IXX . . . L 6 -43.764 10.336 1.319 1 114.41 ? C19 IXX 609 A 1 # _model_server_stats.io_time_ms 84 _model_server_stats.parse_time_ms 27 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 539 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 21 #