data_5CFB # _model_server_result.job_id eIA1Ua0fCLFWpAaIc-iUug _model_server_result.datetime_utc '2024-11-26 18:09:18' _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 5cfb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":501}' # _entry.id 5CFB # _exptl.entry_id 5CFB _exptl.method 'X-RAY DIFFRACTION' # _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 5CFB _cell.length_a 140.242 _cell.length_b 143.198 _cell.length_c 180.054 _cell.Z_PDB 20 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5CFB _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 21' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details pentameric _pdbx_struct_assembly.oligomeric_count 5 _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 ? 3 H N N ? 3 K N N ? 3 L N N ? 3 M N N ? 3 N 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 C 601 NAG 2 n F NAG 2 F 2 NAG C 602 NAG 2 n G NAG 1 G 1 NAG D 601 NAG 2 n G NAG 2 G 2 NAG D 602 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 138 A CYS 138 1_555 A SG CYS 152 A CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf2 A SG CYS 198 A CYS 198 1_555 A SG CYS 209 A CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf3 B SG CYS 138 B CYS 138 1_555 B SG CYS 152 B CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.048 ? disulf ? disulf4 B SG CYS 198 B CYS 198 1_555 B SG CYS 209 B CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.047 ? disulf ? disulf5 C SG CYS 138 C CYS 138 1_555 C SG CYS 152 C CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? disulf ? disulf6 C SG CYS 198 C CYS 198 1_555 C SG CYS 209 C CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.04 ? disulf ? disulf7 D SG CYS 138 D CYS 138 1_555 D SG CYS 152 D CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf8 D SG CYS 198 D CYS 198 1_555 D SG CYS 209 D CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.046 ? disulf ? disulf9 E SG CYS 138 E CYS 138 1_555 E SG CYS 152 E CYS 152 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.054 ? disulf ? disulf10 E SG CYS 198 E CYS 198 1_555 E SG CYS 209 E CYS 209 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? covale ? covale1 A ND2 ASN 38 A ASN 38 1_555 I C1 NAG . A NAG 502 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.453 ? covale ? covale2 B ND2 ASN 38 B ASN 38 1_555 J C1 NAG . B NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.464 ? covale ? covale3 C ND2 ASN 38 C ASN 38 1_555 F C1 NAG . F NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.443 ? covale ? covale4 D ND2 ASN 38 D ASN 38 1_555 G C1 NAG . G NAG 1 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? covale ? covale5 E ND2 ASN 38 E ASN 38 1_555 O C1 NAG . E NAG 601 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.456 ? covale ? covale6 F O4 NAG . F NAG 1 1_555 F C1 NAG . F NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.45 ? covale ? covale7 G O4 NAG . G NAG 1 1_555 G C1 NAG . G NAG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.445 ? # _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 5CFB _atom_sites.fract_transf_matrix[1][1] 0.007131 _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] 0.006983 _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] 0.005554 _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 3 SY9 A 1 501 501 SY9 UNL . I 4 NAG A 1 502 601 NAG NAG . J 4 NAG B 1 601 601 NAG NAG . K 3 SY9 B 1 501 501 SY9 UNL . L 3 SY9 C 1 501 501 SY9 UNL . M 3 SY9 D 1 501 501 SY9 UNL . N 3 SY9 E 1 501 501 SY9 UNL . O 4 NAG E 1 601 601 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 CAV SY9 . . . N 3 120.258 164.318 24.266 1 120.44 ? CAV SY9 501 E 1 HETATM 2 C CAU SY9 . . . N 3 120.125 165.056 22.925 1 121.62 ? CAU SY9 501 E 1 HETATM 3 C CAT SY9 . . . N 3 120.457 164.094 21.794 1 122.21 ? CAT SY9 501 E 1 HETATM 4 C CAN SY9 . . . N 3 119.342 163.055 21.717 1 119.88 ? CAN SY9 501 E 1 HETATM 5 C CAK SY9 . . . N 3 119.151 162.294 23.022 1 117.93 ? CAK SY9 501 E 1 HETATM 6 N NAH SY9 . . . N 3 117.72 162.007 23.005 1 116.57 ? NAH SY9 501 E 1 HETATM 7 C CAA SY9 . . . N 3 117.075 162.618 24.081 1 115.24 ? CAA SY9 501 E 1 HETATM 8 C CAF SY9 . . . N 3 115.721 162.7 24.38 1 117.32 ? CAF SY9 501 E 1 HETATM 9 C CAE SY9 . . . N 3 115.29 163.4 25.502 1 119.1 ? CAE SY9 501 E 1 HETATM 10 C CAD SY9 . . . N 3 116.212 164.039 26.321 1 115.55 ? CAD SY9 501 E 1 HETATM 11 C CAC SY9 . . . N 3 117.565 163.97 26.016 1 114.41 ? CAC SY9 501 E 1 HETATM 12 C CAB SY9 . . . N 3 117.997 163.278 24.892 1 115.28 ? CAB SY9 501 E 1 HETATM 13 C CAG SY9 . . . N 3 119.403 163.035 24.347 1 118.63 ? CAG SY9 501 E 1 HETATM 14 C CAW SY9 . . . N 3 120.176 162.169 25.328 1 120.57 ? CAW SY9 501 E 1 HETATM 15 C CAX SY9 . . . N 3 121.629 162.487 24.999 1 122.14 ? CAX SY9 501 E 1 HETATM 16 N NAY SY9 . . . N 3 121.666 163.892 24.536 1 123.3 ? NAY SY9 501 E 1 HETATM 17 C CAS SY9 . . . N 3 122.558 163.937 23.356 1 125.54 ? CAS SY9 501 E 1 HETATM 18 C CAR SY9 . . . N 3 121.787 163.464 22.125 1 123.51 ? CAR SY9 501 E 1 HETATM 19 C CAQ SY9 . . . N 3 122.403 162.465 21.405 1 124.6 ? CAQ SY9 501 E 1 HETATM 20 C CAP SY9 . . . N 3 121.8 161.925 20.288 1 125.98 ? CAP SY9 501 E 1 HETATM 21 O OAO SY9 . . . N 3 120.589 161.188 20.502 1 126.78 ? OAO SY9 501 E 1 HETATM 22 C CAM SY9 . . . N 3 119.409 162.01 20.573 1 121.8 ? CAM SY9 501 E 1 HETATM 23 C CAL SY9 . . . N 3 118.262 160.954 20.769 1 121.92 ? CAL SY9 501 E 1 HETATM 24 C CAI SY9 . . . N 3 117.245 161.367 21.853 1 119.12 ? CAI SY9 501 E 1 HETATM 25 O OAJ SY9 . . . N 3 116.047 161.118 21.721 1 119.3 ? OAJ SY9 501 E 1 # _model_server_stats.io_time_ms 30 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 14 _model_server_stats.query_time_ms 289 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 25 #