data_3JAD # _model_server_result.job_id 3UEGm3v-3Gxlgmn2Hs3xdA _model_server_result.datetime_utc '2025-02-05 17:10:04' _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 3jad # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"O","auth_seq_id":401}' # _entry.id 3JAD # _exptl.entry_id 3JAD _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 334.412 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description STRYCHNINE _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 3JAD _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB 1 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3JAD _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 _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 ? 3 K N N ? 3 L N N ? 3 M N N ? 3 N N N ? 3 O N N # _pdbx_entity_branch.entity_id 2 _pdbx_entity_branch.type oligosaccharide # _pdbx_entity_branch_link.link_id 1 _pdbx_entity_branch_link.details ? _pdbx_entity_branch_link.entity_id 2 _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 2 n F NAG 1 F 1 NAG A 501 NAG 2 n F NAG 2 F 2 NAG A 502 NAG 2 n G NAG 1 G 1 NAG B 501 NAG 2 n G NAG 2 G 2 NAG B 502 NAG 2 n H NAG 1 H 1 NAG C 501 NAG 2 n H NAG 2 H 2 NAG C 502 NAG 2 n I NAG 1 I 1 NAG D 501 NAG 2 n I NAG 2 I 2 NAG D 502 NAG 2 n J NAG 1 J 1 NAG E 501 NAG 2 n J NAG 2 J 2 NAG E 502 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 190 A CYS 214 1_555 A SG CYS 201 A CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf2 B SG CYS 190 B CYS 214 1_555 B SG CYS 201 B CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf3 C SG CYS 190 C CYS 214 1_555 C SG CYS 201 C CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf4 D SG CYS 190 D CYS 214 1_555 D SG CYS 201 D CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? disulf ? disulf5 E SG CYS 190 E CYS 214 1_555 E SG CYS 201 E CYS 225 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? covale ? covale1 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale2 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.462 ? covale ? covale3 H O4 NAG . H NAG 1 1_555 H C1 NAG . H NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale4 I O4 NAG . I NAG 1 1_555 I C1 NAG . I NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? covale ? covale5 J O4 NAG . J NAG 1 1_555 J C1 NAG . J NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.463 ? # _chem_comp.formula 'C21 H22 N2 O2' _chem_comp.formula_weight 334.412 _chem_comp.id SY9 _chem_comp.mon_nstd_flag . _chem_comp.name STRYCHNINE _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 CAV CAU SY9 sing 318 n n CAV CAG SY9 sing 319 n n CAV NAY SY9 sing 320 n n CAU CAT SY9 sing 321 n n CAT CAN SY9 sing 322 n n CAT CAR SY9 sing 323 n n CAN CAK SY9 sing 324 n n CAN CAM SY9 sing 325 n n CAK NAH SY9 sing 326 n n CAK CAG SY9 sing 327 n n NAH CAA SY9 sing 328 n n NAH CAI SY9 sing 329 n n CAA CAF SY9 sing 330 n y CAA CAB SY9 doub 331 n y CAF CAE SY9 doub 332 n y CAE CAD SY9 sing 333 n y CAD CAC SY9 doub 334 n y CAC CAB SY9 sing 335 n y CAB CAG SY9 sing 336 n n CAG CAW SY9 sing 337 n n CAW CAX SY9 sing 338 n n CAX NAY SY9 sing 339 n n NAY CAS SY9 sing 340 n n CAS CAR SY9 sing 341 n n CAR CAQ SY9 doub 342 n n CAQ CAP SY9 sing 343 n n CAP OAO SY9 sing 344 n n OAO CAM SY9 sing 345 n n CAM CAL SY9 sing 346 n n CAL CAI SY9 sing 347 n n CAI OAJ SY9 doub 348 n n CAV HAV SY9 sing 349 n n CAU HAU1 SY9 sing 350 n n CAU HAU2 SY9 sing 351 n n CAT HAT SY9 sing 352 n n CAN HAN SY9 sing 353 n n CAK HAK SY9 sing 354 n n CAM HAM SY9 sing 355 n n CAF HAF SY9 sing 356 n n CAE HAE SY9 sing 357 n n CAD HAD SY9 sing 358 n n CAC HAC SY9 sing 359 n n CAW HAW1 SY9 sing 360 n n CAW HAW2 SY9 sing 361 n n CAX HAX1 SY9 sing 362 n n CAX HAX2 SY9 sing 363 n n CAS HAS1 SY9 sing 364 n n CAS HAS2 SY9 sing 365 n n CAQ HAQ SY9 sing 366 n n CAP HAP1 SY9 sing 367 n n CAP HAP2 SY9 sing 368 n n CAL HAL1 SY9 sing 369 n n CAL HAL2 SY9 sing 370 n n # _atom_sites.entry_id 3JAD _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 K 3 SY9 A 1 503 402 SY9 SY9 . L 3 SY9 B 1 401 402 SY9 SY9 . M 3 SY9 C 1 401 402 SY9 SY9 . N 3 SY9 D 1 401 402 SY9 SY9 . O 3 SY9 E 1 401 402 SY9 SY9 . # 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 CAV SY9 . . . O 3 168.568 141.992 171.73 1 81.46 ? CAV SY9 401 E 1 HETATM 2 C CAU SY9 . . . O 3 169.387 142.251 170.481 1 81.46 ? CAU SY9 401 E 1 HETATM 3 C CAT SY9 . . . O 3 168.862 143.514 169.797 1 81.46 ? CAT SY9 401 E 1 HETATM 4 C CAN SY9 . . . O 3 168.954 144.756 170.722 1 81.46 ? CAN SY9 401 E 1 HETATM 5 C CAK SY9 . . . O 3 168.103 144.663 171.967 1 81.46 ? CAK SY9 401 E 1 HETATM 6 N NAH SY9 . . . O 3 168.637 145.6 172.99 1 81.46 ? NAH SY9 401 E 1 HETATM 7 C CAA SY9 . . . O 3 168.9 144.894 174.242 1 81.46 ? CAA SY9 401 E 1 HETATM 8 C CAF SY9 . . . O 3 169.378 145.311 175.51 1 81.46 ? CAF SY9 401 E 1 HETATM 9 C CAE SY9 . . . O 3 169.572 144.38 176.576 1 81.46 ? CAE SY9 401 E 1 HETATM 10 C CAD SY9 . . . O 3 169.304 143.008 176.395 1 81.46 ? CAD SY9 401 E 1 HETATM 11 C CAC SY9 . . . O 3 168.834 142.568 175.129 1 81.46 ? CAC SY9 401 E 1 HETATM 12 C CAB SY9 . . . O 3 168.644 143.49 174.073 1 81.46 ? CAB SY9 401 E 1 HETATM 13 C CAG SY9 . . . O 3 168.142 143.228 172.636 1 81.46 ? CAG SY9 401 E 1 HETATM 14 C CAW SY9 . . . O 3 166.698 142.949 172.855 1 81.46 ? CAW SY9 401 E 1 HETATM 15 C CAX SY9 . . . O 3 166.472 141.508 172.408 1 81.46 ? CAX SY9 401 E 1 HETATM 16 N NAY SY9 . . . O 3 167.32 141.345 171.207 1 81.46 ? NAY SY9 401 E 1 HETATM 17 C CAS SY9 . . . O 3 166.828 141.879 169.814 1 81.46 ? CAS SY9 401 E 1 HETATM 18 C CAR SY9 . . . O 3 167.524 143.214 169.208 1 81.46 ? CAR SY9 401 E 1 HETATM 19 C CAQ SY9 . . . O 3 167.338 143.91 168.043 1 81.46 ? CAQ SY9 401 E 1 HETATM 20 C CAP SY9 . . . O 3 167.962 145.313 167.782 1 81.46 ? CAP SY9 401 E 1 HETATM 21 O OAO SY9 . . . O 3 167.838 146.187 168.911 1 81.46 ? OAO SY9 401 E 1 HETATM 22 C CAM SY9 . . . O 3 168.796 146.135 169.982 1 81.46 ? CAM SY9 401 E 1 HETATM 23 C CAL SY9 . . . O 3 168.491 147.276 171.056 1 81.46 ? CAL SY9 401 E 1 HETATM 24 C CAI SY9 . . . O 3 168.868 146.966 172.522 1 81.46 ? CAI SY9 401 E 1 HETATM 25 O OAJ SY9 . . . O 3 169.325 147.804 173.284 1 81.46 ? OAJ SY9 401 E 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 25 #