data_8Y57 # _model_server_result.job_id yXMpv0mBkPTvMR-3Q_1Gcg _model_server_result.datetime_utc '2025-01-10 13:39:21' _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 8y57 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":301}' # _entry.id 8Y57 # _exptl.entry_id 8Y57 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 193.242 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine _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 8Y57 _cell.length_a 254.12 _cell.length_b 254.12 _cell.length_c 254.12 _cell.Z_PDB 96 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Y57 _symmetry.cell_setting ? _symmetry.Int_Tables_number 214 _symmetry.space_group_name_Hall 'I 4bd 2c 3' _symmetry.space_group_name_H-M 'I 41 3 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 E _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 disulf ? disulf1 A SG CYS 26 C CYS 22 1_555 A SG CYS 100 C CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? disulf ? disulf2 A SG CYS 148 C CYS 144 1_555 A SG CYS 204 C CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 B SG CYS 25 D CYS 22 1_555 B SG CYS 93 D CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf4 B SG CYS 141 D CYS 138 1_555 B SG CYS 201 D CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf5 C SG CYS 26 A CYS 22 1_555 C SG CYS 100 A CYS 96 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.033 ? disulf ? disulf6 C SG CYS 148 A CYS 144 1_555 C SG CYS 204 A CYS 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 D SG CYS 25 B CYS 22 1_555 D SG CYS 93 B CYS 90 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf8 D SG CYS 141 B CYS 138 1_555 D SG CYS 201 B CYS 198 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.034 ? # _chem_comp.formula 'C11 H15 N O2' _chem_comp.formula_weight 193.242 _chem_comp.id B41 _chem_comp.mon_nstd_flag . _chem_comp.name (2S)-1-(1,3-benzodioxol-5-yl)-N-methylpropan-2-amine _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '3,4 methylenedioxy-n-methylamphetamine;MDMA;Ecstasy' # 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 O1 CT B41 sing 70 n n O1 CE1 B41 sing 71 n n CT O2 B41 sing 72 n n O2 CZ B41 sing 73 n n CM N B41 sing 74 n n N CA B41 sing 75 n n N HN B41 sing 76 n n C CA B41 sing 77 n n CA CB B41 sing 78 n n CA HA B41 sing 79 n n C H B41 sing 80 n n C HB B41 sing 81 n n C HC B41 sing 82 n n CB CG B41 sing 83 n n CB HBA B41 sing 84 n n CB HBB B41 sing 85 n n CD1 CG B41 doub 86 n y CG CD2 B41 sing 87 n y CD1 CE1 B41 sing 88 n y CD1 HD1 B41 sing 89 n n CD2 CE2 B41 doub 90 n y CD2 HD2 B41 sing 91 n n CE1 CZ B41 doub 92 n y CZ CE2 B41 sing 93 n y CE2 HE2 B41 sing 94 n n CM HM B41 sing 95 n n CM HMA B41 sing 96 n n CM HMB B41 sing 97 n n CT HT B41 sing 98 n n CT HTA B41 sing 99 n n # _atom_sites.entry_id 8Y57 _atom_sites.fract_transf_matrix[1][1] 0.003935 _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] 0.003935 _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] 0.003935 _atom_sites.fract_transf_vector[1] 0 _atom_sites.fract_transf_vector[2] 0 _atom_sites.fract_transf_vector[3] 0 # _pdbx_nonpoly_scheme.asym_id E _pdbx_nonpoly_scheme.entity_id 3 _pdbx_nonpoly_scheme.mon_id B41 _pdbx_nonpoly_scheme.pdb_strand_id B _pdbx_nonpoly_scheme.ndb_seq_num 1 _pdbx_nonpoly_scheme.pdb_seq_num 301 _pdbx_nonpoly_scheme.auth_seq_num 297 _pdbx_nonpoly_scheme.pdb_mon_id B41 _pdbx_nonpoly_scheme.auth_mon_id B41 _pdbx_nonpoly_scheme.pdb_ins_code . # 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 O O1 B41 . . . E 3 -36.961 0.439 44.431 1 88.59 ? O1 B41 301 B 1 HETATM 2 O O2 B41 . . . E 3 -37.723 -0.005 46.492 1 102.81 ? O2 B41 301 B 1 HETATM 3 N N B41 . . . E 3 -42.956 1.445 41.193 1 99.79 ? N B41 301 B 1 HETATM 4 C CA B41 . . . E 3 -42.624 0.818 42.461 1 115.92 ? CA B41 301 B 1 HETATM 5 C C B41 . . . E 3 -43.851 0.111 43.028 1 122.56 ? C B41 301 B 1 HETATM 6 C CB B41 . . . E 3 -41.514 -0.21 42.247 1 102.51 ? CB B41 301 B 1 HETATM 7 C CG B41 . . . E 3 -40.56 -0.176 43.438 1 98.29 ? CG B41 301 B 1 HETATM 8 C CD1 B41 . . . E 3 -39.224 0.131 43.239 1 93.52 ? CD1 B41 301 B 1 HETATM 9 C CD2 B41 . . . E 3 -41.031 -0.451 44.717 1 104.47 ? CD2 B41 301 B 1 HETATM 10 C CE1 B41 . . . E 3 -38.345 0.162 44.332 1 94.39 ? CE1 B41 301 B 1 HETATM 11 C CE2 B41 . . . E 3 -40.163 -0.418 45.797 1 103.43 ? CE2 B41 301 B 1 HETATM 12 C CZ B41 . . . E 3 -38.811 -0.108 45.596 1 98.86 ? CZ B41 301 B 1 HETATM 13 C CM B41 . . . E 3 -43.379 2.815 41.431 1 99.14 ? CM B41 301 B 1 HETATM 14 C CT B41 . . . E 3 -36.549 0.085 45.727 1 87.79 ? CT B41 301 B 1 HETATM 15 H HN B41 . . . E 3 -43.698 0.938 40.753 1 119.75 ? HN B41 301 B 1 HETATM 16 H HA B41 . . . E 3 -42.292 1.581 43.155 1 139.1 ? HA B41 301 B 1 HETATM 17 H H B41 . . . E 3 -43.572 -0.437 43.921 1 147.07 ? H B41 301 B 1 HETATM 18 H HB B41 . . . E 3 -44.609 0.847 43.276 1 147.07 ? HB B41 301 B 1 HETATM 19 H HC B41 . . . E 3 -44.245 -0.578 42.288 1 147.07 ? HC B41 301 B 1 HETATM 20 H HBA B41 . . . E 3 -40.97 0.029 41.34 1 123.01 ? HBA B41 301 B 1 HETATM 21 H HBB B41 . . . E 3 -41.949 -1.199 42.158 1 123.01 ? HBB B41 301 B 1 HETATM 22 H HD1 B41 . . . E 3 -38.858 0.346 42.243 1 112.23 ? HD1 B41 301 B 1 HETATM 23 H HD2 B41 . . . E 3 -42.076 -0.691 44.869 1 125.36 ? HD2 B41 301 B 1 HETATM 24 H HE2 B41 . . . E 3 -40.529 -0.631 46.794 1 124.12 ? HE2 B41 301 B 1 HETATM 25 H HM B41 . . . E 3 -42.537 3.396 41.796 1 118.97 ? HM B41 301 B 1 HETATM 26 H HMA B41 . . . E 3 -44.174 2.825 42.171 1 118.97 ? HMA B41 301 B 1 HETATM 27 H HMB B41 . . . E 3 -43.742 3.248 40.503 1 118.97 ? HMB B41 301 B 1 HETATM 28 H HT B41 . . . E 3 -35.898 0.852 46.134 1 105.35 ? HT B41 301 B 1 HETATM 29 H HTA B41 . . . E 3 -36.042 -0.873 45.708 1 105.35 ? HTA B41 301 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 11 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 236 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 29 #