data_6RUQ # _model_server_result.job_id CABQQD6IlcmN9n_oMninqA _model_server_result.datetime_utc '2025-02-16 16:18:10' _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 6ruq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":901}' # _entry.id 6RUQ # _exptl.entry_id 6RUQ _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 352.387 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (8R)-5-(4-aminophenyl)-N,8-dimethyl-8,9-dihydro-2H,7H-[1,3]dioxolo[4,5-h][2,3]benzodiazepine-7-carboxamide _entity.pdbx_number_of_molecules 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 94.264 _cell.angle_gamma 90 _cell.entry_id 6RUQ _cell.length_a 91.773 _cell.length_b 306.596 _cell.length_c 107.728 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 6RUQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall 'P 2yb' _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _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,F,G,H,I,J,K,L,M,N,O _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 H N N ? 4 J N N ? 4 L N N ? 4 N N N # loop_ _pdbx_entity_branch.entity_id _pdbx_entity_branch.type 2 oligosaccharide 3 oligosaccharide # loop_ _pdbx_entity_branch_link.link_id _pdbx_entity_branch_link.details _pdbx_entity_branch_link.entity_id _pdbx_entity_branch_link.entity_branch_list_num_1 _pdbx_entity_branch_link.entity_branch_list_num_2 _pdbx_entity_branch_link.comp_id_1 _pdbx_entity_branch_link.comp_id_2 _pdbx_entity_branch_link.atom_id_1 _pdbx_entity_branch_link.leaving_atom_id_1 _pdbx_entity_branch_link.atom_stereo_config_1 _pdbx_entity_branch_link.atom_id_2 _pdbx_entity_branch_link.leaving_atom_id_2 _pdbx_entity_branch_link.atom_stereo_config_2 _pdbx_entity_branch_link.value_order 1 ? 2 2 1 NAG NAG C1 O1 . O4 HO4 . sing 2 ? 2 3 2 BMA NAG C1 O1 . O4 HO4 . sing 3 ? 3 2 1 NAG NAG C1 O1 . O4 HO4 . sing 4 ? 3 3 2 BMA NAG C1 O1 . O4 HO4 . sing 5 ? 3 4 3 BMA BMA C1 O1 . O3 HO3 . 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 2 n E NAG 1 E 1 NAG H 834 NAG 2 n E NAG 2 E 2 NAG H 835 NAG 2 n E BMA 3 E 3 BMA H 836 BMA 3 n F NAG 1 F 1 NAG G 834 NAG 3 n F NAG 2 F 2 NAG G 835 NAG 3 n F BMA 3 F 3 BMA G 836 BMA 3 n F BMA 4 F 4 BMA G 837 BMA 2 n G NAG 1 G 1 NAG I 834 NAG 2 n G NAG 2 G 2 NAG I 835 NAG 2 n G BMA 3 G 3 BMA I 836 BMA # 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 54 A CYS 63 1_555 A SG CYS 306 A CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? disulf ? disulf2 A SG CYS 709 A CYS 718 1_555 A SG CYS 764 A CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? disulf ? disulf3 B SG CYS 54 B CYS 63 1_555 B SG CYS 306 B CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf4 B SG CYS 709 B CYS 718 1_555 B SG CYS 764 B CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 C SG CYS 54 C CYS 63 1_555 C SG CYS 306 C CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf6 C SG CYS 709 C CYS 718 1_555 C SG CYS 764 C CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.029 ? disulf ? disulf7 D SG CYS 54 D CYS 63 1_555 D SG CYS 306 D CYS 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf8 D SG CYS 709 D CYS 718 1_555 D SG CYS 764 D CYS 773 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.032 ? covale ? covale1 A ND2 ASN 346 A ASN 355 1_555 E C1 NAG . E NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale2 B ND2 ASN 346 B ASN 355 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.452 ? covale ? covale3 C ND2 ASN 346 C ASN 355 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale4 E O4 NAG . E NAG 1 1_555 E C1 NAG . E NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale5 E O4 NAG . E NAG 2 1_555 E C1 BMA . E BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale6 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale7 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale8 F O3 BMA . F BMA 3 1_555 F C1 BMA . F BMA 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.448 ? covale ? covale9 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale10 G O4 NAG . G NAG 2 1_555 G C1 BMA . G BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _chem_comp.formula 'C19 H20 N4 O3' _chem_comp.formula_weight 352.387 _chem_comp.id GYK _chem_comp.mon_nstd_flag . _chem_comp.name (8R)-5-(4-aminophenyl)-N,8-dimethyl-8,9-dihydro-2H,7H-[1,3]dioxolo[4,5-h][2,3]benzodiazepine-7-carboxamide _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 N23 C20 GYK sing 153 n n C20 C21 GYK doub 154 n y C20 C19 GYK sing 155 n y C21 C22 GYK sing 156 n y C19 C18 GYK doub 157 n y O24 C25 GYK sing 158 n n O24 C07 GYK sing 159 n n C25 O26 GYK sing 160 n n C22 C17 GYK doub 161 n y C18 C17 GYK sing 162 n y C07 C08 GYK doub 163 n y C07 C06 GYK sing 164 n y C08 C09 GYK sing 165 n y C17 C10 GYK sing 166 n n O26 C06 GYK sing 167 n n C06 C05 GYK doub 168 n y C09 C10 GYK sing 169 n n C09 C04 GYK doub 170 n y C10 N11 GYK doub 171 n n C05 C04 GYK sing 172 n y C04 C03 GYK sing 173 n n N11 N12 GYK sing 174 n n C03 C02 GYK sing 175 n n N12 C02 GYK sing 176 n n N12 C13 GYK sing 177 n n N15 C13 GYK sing 178 n n N15 C16 GYK sing 179 n n C01 C02 GYK sing 180 n n C13 O14 GYK doub 181 n n C01 H1 GYK sing 182 n n C01 H2 GYK sing 183 n n C01 H3 GYK sing 184 n n C02 H4 GYK sing 185 n n C03 H5 GYK sing 186 n n C03 H6 GYK sing 187 n n C05 H7 GYK sing 188 n n C08 H8 GYK sing 189 n n N15 H11 GYK sing 190 n n C16 H12 GYK sing 191 n n C16 H13 GYK sing 192 n n C16 H14 GYK sing 193 n n C18 H15 GYK sing 194 n n C19 H16 GYK sing 195 n n C21 H17 GYK sing 196 n n C22 H18 GYK sing 197 n n N23 H19 GYK sing 198 n n N23 H20 GYK sing 199 n n C25 H21 GYK sing 200 n n C25 H9 GYK sing 201 n n # _atom_sites.entry_id 6RUQ _atom_sites.fract_transf_matrix[1][1] 0.010896 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000812 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.003262 _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] 0.009308 _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 H 4 GYK A 1 901 1 GYK GYK . I 5 ZK1 A 1 902 2 ZK1 ZK1 . J 4 GYK B 1 901 3 GYK GYK . K 5 ZK1 B 1 902 3 ZK1 ZK1 . L 4 GYK C 1 901 2 GYK GYK . M 5 ZK1 C 1 902 1 ZK1 ZK1 . N 4 GYK D 1 901 4 GYK GYK . O 5 ZK1 D 1 902 4 ZK1 ZK1 . # 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 C01 GYK . . . N 4 -66.088 -32.649 -19.972 1 223.24 ? C01 GYK 901 D 1 HETATM 2 C C02 GYK . . . N 4 -64.694 -33.297 -19.994 1 230.8 ? C02 GYK 901 D 1 HETATM 3 C C03 GYK . . . N 4 -64.081 -33.214 -18.595 1 226.26 ? C03 GYK 901 D 1 HETATM 4 C C04 GYK . . . N 4 -64.142 -31.806 -17.986 1 226.25 ? C04 GYK 901 D 1 HETATM 5 C C05 GYK . . . N 4 -64.89 -31.683 -16.772 1 238.98 ? C05 GYK 901 D 1 HETATM 6 C C06 GYK . . . N 4 -64.993 -30.42 -16.147 1 257 ? C06 GYK 901 D 1 HETATM 7 C C07 GYK . . . N 4 -64.357 -29.303 -16.723 1 253.64 ? C07 GYK 901 D 1 HETATM 8 C C08 GYK . . . N 4 -63.609 -29.434 -17.933 1 244.42 ? C08 GYK 901 D 1 HETATM 9 C C09 GYK . . . N 4 -63.503 -30.705 -18.568 1 232.86 ? C09 GYK 901 D 1 HETATM 10 C C10 GYK . . . N 4 -62.686 -30.865 -19.899 1 238.72 ? C10 GYK 901 D 1 HETATM 11 N N11 GYK . . . N 4 -63.561 -31.228 -20.998 1 245.55 ? N11 GYK 901 D 1 HETATM 12 N N12 GYK . . . N 4 -63.865 -32.598 -20.959 1 238.66 ? N12 GYK 901 D 1 HETATM 13 C C13 GYK . . . N 4 -63.271 -33.427 -21.997 1 240.23 ? C13 GYK 901 D 1 HETATM 14 O O14 GYK . . . N 4 -63.487 -34.591 -22.013 1 241.38 ? O14 GYK 901 D 1 HETATM 15 N N15 GYK . . . N 4 -62.421 -32.831 -23.009 1 236.59 ? N15 GYK 901 D 1 HETATM 16 C C16 GYK . . . N 4 -61.838 -33.669 -24.042 1 240.69 ? C16 GYK 901 D 1 HETATM 17 C C17 GYK . . . N 4 -61.774 -29.729 -20.321 1 253.41 ? C17 GYK 901 D 1 HETATM 18 C C18 GYK . . . N 4 -60.4 -29.907 -20.232 1 254.42 ? C18 GYK 901 D 1 HETATM 19 C C19 GYK . . . N 4 -59.533 -28.895 -20.609 1 256.51 ? C19 GYK 901 D 1 HETATM 20 C C20 GYK . . . N 4 -60.033 -27.696 -21.088 1 265 ? C20 GYK 901 D 1 HETATM 21 C C21 GYK . . . N 4 -61.4 -27.514 -21.187 1 270.6 ? C21 GYK 901 D 1 HETATM 22 C C22 GYK . . . N 4 -62.265 -28.529 -20.809 1 264.55 ? C22 GYK 901 D 1 HETATM 23 N N23 GYK . . . N 4 -59.126 -26.637 -21.485 1 262.26 ? N23 GYK 901 D 1 HETATM 24 O O24 GYK . . . N 4 -64.657 -28.253 -15.87 1 261.27 ? O24 GYK 901 D 1 HETATM 25 C C25 GYK . . . N 4 -65.404 -28.673 -14.862 1 264.73 ? C25 GYK 901 D 1 HETATM 26 O O26 GYK . . . N 4 -65.627 -29.967 -14.995 1 275.17 ? O26 GYK 901 D 1 # _model_server_stats.io_time_ms 33 _model_server_stats.parse_time_ms 14 _model_server_stats.create_model_time_ms 41 _model_server_stats.query_time_ms 274 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 26 #