data_6Y1Z # _model_server_result.job_id F555kCvBigEipTR6W5M3xw _model_server_result.datetime_utc '2025-02-05 17:00:51' _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 6y1z # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"BA","auth_seq_id":501}' # _entry.id 6Y1Z # _exptl.entry_id 6Y1Z _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 296.407 _entity.id 7 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description (3~{a}~{S})-2-[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]-3~{a},4,5,6-tetrahydro-3~{H}-benzo[de]isoquinolin-1-one _entity.pdbx_number_of_molecules 5 _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 6Y1Z _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 6Y1Z _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _pdbx_struct_assembly.details author_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,U,V,W,X,Y,Z,AA,BA,CA,DA,EA,FA,GA,HA,IA _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 ? _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 ? 7 S N N ? 7 W N N ? 7 AA N N ? 7 BA N N ? 7 FA 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 # 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 F NAG 1 F 1 NAG A 505 NAG 2 n F NAG 2 F 2 NAG A 504 NAG 2 n F BMA 3 F 3 BMA A 503 BMA 3 n G NAG 1 G 1 NAG A 506 NAG 3 n G NAG 2 G 2 NAG A 507 NAG 2 n H NAG 1 H 1 NAG D 505 NAG 2 n H NAG 2 H 2 NAG D 504 NAG 2 n H BMA 3 H 3 BMA D 503 BMA 3 n I NAG 1 I 1 NAG D 506 NAG 3 n I NAG 2 I 2 NAG D 507 NAG 2 n J NAG 1 J 1 NAG B 505 NAG 2 n J NAG 2 J 2 NAG B 504 NAG 2 n J BMA 3 J 3 BMA B 503 BMA 3 n K NAG 1 K 1 NAG B 506 NAG 3 n K NAG 2 K 2 NAG B 507 NAG 2 n L NAG 1 L 1 NAG C 505 NAG 2 n L NAG 2 L 2 NAG C 504 NAG 2 n L BMA 3 L 3 BMA C 503 BMA 3 n M NAG 1 M 1 NAG C 506 NAG 3 n M NAG 2 M 2 NAG C 507 NAG 2 n N NAG 1 N 1 NAG E 505 NAG 2 n N NAG 2 N 2 NAG E 504 NAG 2 n N BMA 3 N 3 BMA E 503 BMA 3 n O NAG 1 O 1 NAG E 506 NAG 3 n O NAG 2 O 2 NAG E 507 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 239 A CYS 135 1_555 A SG CYS 253 A CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf2 B SG CYS 239 D CYS 135 1_555 B SG CYS 253 D CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf3 C SG CYS 239 B CYS 135 1_555 C SG CYS 253 B CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf4 D SG CYS 239 C CYS 135 1_555 D SG CYS 253 C CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.03 ? disulf ? disulf5 E SG CYS 239 E CYS 135 1_555 E SG CYS 253 E CYS 149 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.031 ? covale ? covale1 A ND2 ASN 186 A ASN 82 1_555 R C1 NAG . A NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale2 A ND2 ASN 252 A ASN 148 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale3 A ND2 ASN 268 A ASN 164 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.438 ? covale ? covale4 B ND2 ASN 186 D ASN 82 1_555 V C1 NAG . D NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale5 B ND2 ASN 252 D ASN 148 1_555 I C1 NAG . I NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale6 B ND2 ASN 268 D ASN 164 1_555 H C1 NAG . H NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale7 C ND2 ASN 186 B ASN 82 1_555 Z C1 NAG . B NAG 503 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale8 C ND2 ASN 252 B ASN 148 1_555 K C1 NAG . K NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale9 C ND2 ASN 268 B ASN 164 1_555 J C1 NAG . J NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale10 D ND2 ASN 186 C ASN 82 1_555 EA C1 NAG . C NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale11 D ND2 ASN 252 C ASN 148 1_555 M C1 NAG . M NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale12 D ND2 ASN 268 C ASN 164 1_555 L C1 NAG . L NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale13 E ND2 ASN 186 E ASN 82 1_555 IA C1 NAG . E NAG 504 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale14 E ND2 ASN 252 E ASN 148 1_555 O C1 NAG . O NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.44 ? covale ? covale15 E ND2 ASN 268 E ASN 164 1_555 N C1 NAG . N NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.439 ? covale ? covale16 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale17 F O4 NAG . F NAG 2 1_555 F C1 BMA . F BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale18 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.442 ? covale ? covale19 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale20 H O4 NAG . H NAG 2 1_555 H C1 BMA . H BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale21 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale22 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale23 J O4 NAG . J NAG 2 1_555 J C1 BMA . J BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale24 K O4 NAG . K NAG 1 1_555 K C1 NAG . K NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale25 L O4 NAG . L NAG 1 1_555 L C1 NAG . L NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale26 L O4 NAG . L NAG 2 1_555 L C1 BMA . L BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale27 M O4 NAG . M NAG 1 1_555 M C1 NAG . M NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? covale ? covale28 N O4 NAG . N NAG 1 1_555 N C1 NAG . N NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.444 ? covale ? covale29 N O4 NAG . N NAG 2 1_555 N C1 BMA . N BMA 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? covale ? covale30 O O4 NAG . O NAG 1 1_555 O C1 NAG . O NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.441 ? # _chem_comp.formula 'C19 H24 N2 O' _chem_comp.formula_weight 296.407 _chem_comp.id O7B _chem_comp.mon_nstd_flag . _chem_comp.name (3~{a}~{S})-2-[(3~{S})-1-azabicyclo[2.2.2]octan-3-yl]-3~{a},4,5,6-tetrahydro-3~{H}-benzo[de]isoquinolin-1-one _chem_comp.type non-polymer _chem_comp.pdbx_synonyms Palonosetron;Aloxi # 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 C12 O7B doub 289 n y C11 C10 O7B sing 290 n y C02 C01 O7B sing 291 n n C02 C03 O7B sing 292 n n C14 C10 O7B sing 293 n n C14 C01 O7B sing 294 n n C12 C13 O7B sing 295 n y C04 N05 O7B sing 296 n n C04 C03 O7B sing 297 n n C10 C09 O7B doub 298 n y C13 C08 O7B doub 299 n y C20 C21 O7B sing 300 n n C20 C15 O7B sing 301 n n C20 C19 O7B sing 302 n n C09 C08 O7B sing 303 n y C09 C03 O7B sing 304 n n C08 C06 O7B sing 305 n n C21 C22 O7B sing 306 n n N05 C06 O7B sing 307 n n N05 C15 O7B sing 308 n n C06 O07 O7B doub 309 n n C15 C16 O7B sing 310 n n C19 C18 O7B sing 311 n n C22 N17 O7B sing 312 n n C16 N17 O7B sing 313 n n C18 N17 O7B sing 314 n n C01 H1 O7B sing 315 n n C01 H2 O7B sing 316 n n C02 H3 O7B sing 317 n n C02 H4 O7B sing 318 n n C03 H5 O7B sing 319 n n C04 H6 O7B sing 320 n n C04 H7 O7B sing 321 n n C11 H8 O7B sing 322 n n C12 H9 O7B sing 323 n n C13 H10 O7B sing 324 n n C14 H11 O7B sing 325 n n C14 H12 O7B sing 326 n n C15 H13 O7B sing 327 n n C16 H14 O7B sing 328 n n C16 H15 O7B sing 329 n n C18 H16 O7B sing 330 n n C18 H17 O7B sing 331 n n C19 H18 O7B sing 332 n n C19 H19 O7B sing 333 n n C20 H20 O7B sing 334 n n C21 H21 O7B sing 335 n n C21 H22 O7B sing 336 n n C22 H23 O7B sing 337 n n C22 H24 O7B sing 338 n n # _atom_sites.entry_id 6Y1Z _atom_sites.fract_transf_matrix[1][1] 1 _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] 1 _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] 1 _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 P 4 TRP A 1 501 459 TRP TRP . Q 5 HIS A 1 502 460 HIS HIS . R 6 NAG A 1 503 501 NAG NAG . S 7 O7B A 1 504 903 O7B PAL . T 4 TRP D 1 501 459 TRP TRP . U 5 HIS D 1 502 460 HIS HIS . V 6 NAG D 1 503 501 NAG NAG . W 7 O7B D 1 504 903 O7B PAL . X 4 TRP B 1 501 459 TRP TRP . Y 5 HIS B 1 502 460 HIS HIS . Z 6 NAG B 1 503 501 NAG NAG . AA 7 O7B B 1 504 903 O7B PAL . BA 7 O7B C 1 501 903 O7B PAL . CA 4 TRP C 1 502 459 TRP TRP . DA 5 HIS C 1 503 460 HIS HIS . EA 6 NAG C 1 504 501 NAG NAG . FA 7 O7B E 1 501 903 O7B PAL . GA 4 TRP E 1 502 459 TRP TRP . HA 5 HIS E 1 503 460 HIS HIS . IA 6 NAG E 1 504 501 NAG NAG . # 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 O7B . . . BA 7 101.294 143.137 158.754 1 74.82 ? C01 O7B 501 C 1 HETATM 2 C C02 O7B . . . BA 7 102.619 143.719 158.293 1 74.82 ? C02 O7B 501 C 1 HETATM 3 C C03 O7B . . . BA 7 103.794 143.001 158.947 1 74.82 ? C03 O7B 501 C 1 HETATM 4 C C04 O7B . . . BA 7 105.123 143.428 158.331 1 74.82 ? C04 O7B 501 C 1 HETATM 5 C C06 O7B . . . BA 7 106.108 141.35 159.182 1 74.82 ? C06 O7B 501 C 1 HETATM 6 C C08 O7B . . . BA 7 104.815 140.739 158.831 1 74.82 ? C08 O7B 501 C 1 HETATM 7 C C09 O7B . . . BA 7 103.655 141.514 158.725 1 74.82 ? C09 O7B 501 C 1 HETATM 8 C C10 O7B . . . BA 7 102.431 140.908 158.418 1 74.82 ? C10 O7B 501 C 1 HETATM 9 C C11 O7B . . . BA 7 102.395 139.53 158.225 1 74.82 ? C11 O7B 501 C 1 HETATM 10 C C12 O7B . . . BA 7 103.544 138.767 158.325 1 74.82 ? C12 O7B 501 C 1 HETATM 11 C C13 O7B . . . BA 7 104.755 139.363 158.625 1 74.82 ? C13 O7B 501 C 1 HETATM 12 C C14 O7B . . . BA 7 101.167 141.719 158.274 1 74.82 ? C14 O7B 501 C 1 HETATM 13 C C15 O7B . . . BA 7 107.439 143.486 159.223 1 74.82 ? C15 O7B 501 C 1 HETATM 14 C C16 O7B . . . BA 7 108.099 143.312 160.6 1 74.82 ? C16 O7B 501 C 1 HETATM 15 C C18 O7B . . . BA 7 107.482 145.559 161.338 1 74.82 ? C18 O7B 501 C 1 HETATM 16 C C19 O7B . . . BA 7 106.675 145.735 160.062 1 74.82 ? C19 O7B 501 C 1 HETATM 17 C C20 O7B . . . BA 7 107.372 144.99 158.923 1 74.82 ? C20 O7B 501 C 1 HETATM 18 C C21 O7B . . . BA 7 108.79 145.529 158.792 1 74.82 ? C21 O7B 501 C 1 HETATM 19 C C22 O7B . . . BA 7 109.55 145.23 160.076 1 74.82 ? C22 O7B 501 C 1 HETATM 20 N N05 O7B . . . BA 7 106.225 142.681 158.936 1 74.82 ? N05 O7B 501 C 1 HETATM 21 N N17 O7B . . . BA 7 108.621 144.629 161.085 1 74.82 ? N17 O7B 501 C 1 HETATM 22 O O07 O7B . . . BA 7 107.027 140.695 159.634 1 74.82 ? O07 O7B 501 C 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 13 _model_server_stats.create_model_time_ms 48 _model_server_stats.query_time_ms 442 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 22 #