data_8Y5G # _model_server_result.job_id XQgtQeqd6CjDhQK1yYHxCg _model_server_result.datetime_utc '2024-11-14 00:04:35' _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 8y5g # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":301}' # _entry.id 8Y5G # _exptl.entry_id 8Y5G _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 145.246 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMIDINE _entity.pdbx_number_of_molecules 1 _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 8Y5G _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 8Y5G _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 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 _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 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id G _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # 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 metalc ? metalc1 A O PHE 331 A PHE 345 1_555 E MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.321 ? metalc ? metalc2 A OD1 ASP 334 A ASP 348 1_555 F MG MG . A MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc3 D O PHE 330 D PHE 345 1_555 H MG MG . D MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.191 ? metalc ? metalc4 D OD1 ASP 333 D ASP 348 1_555 I MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.803 ? metalc ? metalc5 D OD2 ASP 333 D ASP 348 1_555 I MG MG . D MG 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.131 ? # _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 288 n n N1 HN11 SPD sing 289 n n N1 HN12 SPD sing 290 n n C2 C3 SPD sing 291 n n C2 H21 SPD sing 292 n n C2 H22 SPD sing 293 n n C3 C4 SPD sing 294 n n C3 H31 SPD sing 295 n n C3 H32 SPD sing 296 n n C4 C5 SPD sing 297 n n C4 H41 SPD sing 298 n n C4 H42 SPD sing 299 n n C5 N6 SPD sing 300 n n C5 H51 SPD sing 301 n n C5 H52 SPD sing 302 n n N6 C7 SPD sing 303 n n N6 HN6 SPD sing 304 n n C7 C8 SPD sing 305 n n C7 H71 SPD sing 306 n n C7 H72 SPD sing 307 n n C8 C9 SPD sing 308 n n C8 H81 SPD sing 309 n n C8 H82 SPD sing 310 n n C9 N10 SPD sing 311 n n C9 H91 SPD sing 312 n n C9 H92 SPD sing 313 n n N10 H101 SPD sing 314 n n N10 H102 SPD sing 315 n n # _atom_sites.entry_id 8Y5G _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 E 5 MG A 1 401 403 MG MG . F 5 MG A 1 402 404 MG MG . G 6 SPD B 1 301 302 SPD SPD . H 5 MG D 1 401 403 MG MG . I 5 MG D 1 402 404 MG MG . # 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 . . . G 6 90.621 98.172 77.545 1 77.62 ? N1 SPD 301 B 1 HETATM 2 C C2 SPD . . . G 6 91.667 98.932 78.202 1 77.73 ? C2 SPD 301 B 1 HETATM 3 C C3 SPD . . . G 6 93.025 98.313 77.882 1 77.56 ? C3 SPD 301 B 1 HETATM 4 C C4 SPD . . . G 6 93.115 98.04 76.384 1 77.62 ? C4 SPD 301 B 1 HETATM 5 C C5 SPD . . . G 6 94.576 98.04 75.949 1 77.54 ? C5 SPD 301 B 1 HETATM 6 N N6 SPD . . . G 6 94.714 97.245 74.744 1 77.26 ? N6 SPD 301 B 1 HETATM 7 C C7 SPD . . . G 6 96.031 97.452 74.173 1 77.59 ? C7 SPD 301 B 1 HETATM 8 C C8 SPD . . . G 6 96.225 96.498 72.999 1 77.5 ? C8 SPD 301 B 1 HETATM 9 C C9 SPD . . . G 6 97.319 97.038 72.084 1 77.72 ? C9 SPD 301 B 1 HETATM 10 N N10 SPD . . . G 6 97.578 96.086 71.021 1 76.99 ? N10 SPD 301 B 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 144 _model_server_stats.create_model_time_ms 155 _model_server_stats.query_time_ms 291 _model_server_stats.encode_time_ms 6 _model_server_stats.element_count 10 #