data_8QZX # _model_server_result.job_id AZYCMwImhBLEH3yKX4RB0A _model_server_result.datetime_utc '2024-10-10 12:23:10' _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 8qzx # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"J","auth_seq_id":402}' # _entry.id 8QZX # _exptl.entry_id 8QZX _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 145.246 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMIDINE _entity.pdbx_number_of_molecules 3 _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 8QZX _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8QZX _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 _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 ? 4 G N N ? 4 J N N ? 4 K N N # _chem_comp.formula 'C7 H19 N3' _chem_comp.formula_weight 145.246 _chem_comp.id SPD _chem_comp.mon_nstd_flag . _chem_comp.name SPERMIDINE _chem_comp.type non-polymer _chem_comp.pdbx_synonyms N-(2-AMINO-PROPYL)-1,4-DIAMINOBUTANE;PA(34) # 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 N1 C2 SPD sing 363 n n N1 HN11 SPD sing 364 n n N1 HN12 SPD sing 365 n n C2 C3 SPD sing 366 n n C2 H21 SPD sing 367 n n C2 H22 SPD sing 368 n n C3 C4 SPD sing 369 n n C3 H31 SPD sing 370 n n C3 H32 SPD sing 371 n n C4 C5 SPD sing 372 n n C4 H41 SPD sing 373 n n C4 H42 SPD sing 374 n n C5 N6 SPD sing 375 n n C5 H51 SPD sing 376 n n C5 H52 SPD sing 377 n n N6 C7 SPD sing 378 n n N6 HN6 SPD sing 379 n n C7 C8 SPD sing 380 n n C7 H71 SPD sing 381 n n C7 H72 SPD sing 382 n n C8 C9 SPD sing 383 n n C8 H81 SPD sing 384 n n C8 H82 SPD sing 385 n n C9 N10 SPD sing 386 n n C9 H91 SPD sing 387 n n C9 H92 SPD sing 388 n n N10 H101 SPD sing 389 n n N10 H102 SPD sing 390 n n # _atom_sites.entry_id 8QZX _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 F 3 NAD A 1 401 405 NAD NAD . G 4 SPD A 1 402 406 SPD SPD . H 3 NAD B 1 401 404 NAD NAD . I 3 NAD C 1 401 404 NAD NAD . J 4 SPD C 1 402 405 SPD SPD . K 4 SPD D 1 401 406 SPD SPD . L 3 NAD D 1 402 404 NAD NAD . # 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 N N1 SPD . . . J 4 133.164 151.374 119.294 1 35.95 ? N1 SPD 402 C 1 HETATM 2 C C2 SPD . . . J 4 134.596 151.588 119.523 1 35.95 ? C2 SPD 402 C 1 HETATM 3 C C3 SPD . . . J 4 135.351 150.368 120.027 1 35.95 ? C3 SPD 402 C 1 HETATM 4 C C4 SPD . . . J 4 136.84 150.617 120.196 1 35.95 ? C4 SPD 402 C 1 HETATM 5 C C5 SPD . . . J 4 137.143 151.631 121.287 1 35.95 ? C5 SPD 402 C 1 HETATM 6 N N6 SPD . . . J 4 136.866 151.096 122.62 1 35.95 ? N6 SPD 402 C 1 HETATM 7 C C7 SPD . . . J 4 137.091 152.057 123.699 1 35.95 ? C7 SPD 402 C 1 HETATM 8 C C8 SPD . . . J 4 137.294 151.363 125.022 1 35.95 ? C8 SPD 402 C 1 HETATM 9 C C9 SPD . . . J 4 137.578 152.292 126.165 1 35.95 ? C9 SPD 402 C 1 HETATM 10 N N10 SPD . . . J 4 137.925 151.557 127.384 1 35.95 ? N10 SPD 402 C 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 13 _model_server_stats.query_time_ms 280 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 10 #