data_7M5Y # _model_server_result.job_id q2NWncWemih24xP8hwu8uA _model_server_result.datetime_utc '2024-11-21 14:19:29' _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 7m5y # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"X","auth_seq_id":1223}' # _entry.id 7M5Y # _exptl.entry_id 7M5Y _exptl.method 'ELECTRON MICROSCOPY' # _entity.details ? _entity.formula_weight 206.372 _entity.id 11 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'SPERMINE (FULLY PROTONATED FORM)' _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 7M5Y _cell.length_a 1 _cell.length_b 1 _cell.length_c 1 _cell.Z_PDB ? _cell.pdbx_unique_axis ? # _symmetry.entry_id 7M5Y _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 _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 # _struct_asym.details ? _struct_asym.entity_id 11 _struct_asym.id X _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 covale ? covale1 A ND2 ASN 1033 A ASN 1033 1_555 W C1 NAG . A NAG 1222 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.446 ? metalc ? metalc1 A OD2 ASP 513 A ASP 513 1_555 B MG MG . A MG 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.169 ? metalc ? metalc2 A OD1 ASP 513 A ASP 513 1_555 C MG MF4 . A MF4 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.94 ? metalc ? metalc3 A O THR 515 A THR 515 1_555 B MG MG . A MG 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.421 ? metalc ? metalc4 A OD1 ASP 878 A ASP 878 1_555 B MG MG . A MG 1201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.503 ? # _chem_comp.formula 'C10 H30 N4 4' _chem_comp.formula_weight 206.372 _chem_comp.id SPK _chem_comp.mon_nstd_flag . _chem_comp.name 'SPERMINE (FULLY PROTONATED FORM)' _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 N1 C2 SPK sing 690 n n N1 H1A SPK sing 691 n n N1 H1B SPK sing 692 n n N1 H1C SPK sing 693 n n C2 C3 SPK sing 694 n n C2 H2A SPK sing 695 n n C2 H2B SPK sing 696 n n C3 C4 SPK sing 697 n n C3 H3A SPK sing 698 n n C3 H3B SPK sing 699 n n C4 N5 SPK sing 700 n n C4 H4A SPK sing 701 n n C4 H4B SPK sing 702 n n N5 C6 SPK sing 703 n n N5 H5A SPK sing 704 n n N5 H5B SPK sing 705 n n C6 C7 SPK sing 706 n n C6 H6A SPK sing 707 n n C6 H6B SPK sing 708 n n C7 C8 SPK sing 709 n n C7 H7A SPK sing 710 n n C7 H7B SPK sing 711 n n C8 C9 SPK sing 712 n n C8 H8A SPK sing 713 n n C8 H8B SPK sing 714 n n C9 N10 SPK sing 715 n n C9 H9A SPK sing 716 n n C9 H9B SPK sing 717 n n N10 C11 SPK sing 718 n n N10 H101 SPK sing 719 n n N10 H102 SPK sing 720 n n C11 C12 SPK sing 721 n n C11 H111 SPK sing 722 n n C11 H112 SPK sing 723 n n C12 C13 SPK sing 724 n n C12 H121 SPK sing 725 n n C12 H122 SPK sing 726 n n C13 N14 SPK sing 727 n n C13 H131 SPK sing 728 n n C13 H132 SPK sing 729 n n N14 H141 SPK sing 730 n n N14 H142 SPK sing 731 n n N14 H143 SPK sing 732 n n # _atom_sites.entry_id 7M5Y _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 B 2 MG A 1 1201 1201 MG MG . C 3 MF4 A 1 1202 1202 MF4 MF4 . D 4 Y01 A 1 1203 1203 Y01 Y01 . E 5 LMT A 1 1204 1204 LMT LMT . F 4 Y01 A 1 1205 1205 Y01 Y01 . G 6 CLR A 1 1206 1206 CLR CLR . H 6 CLR A 1 1207 1207 CLR CLR . I 4 Y01 A 1 1208 1208 Y01 Y01 . J 7 D10 A 1 1209 1209 D10 D10 . K 7 D10 A 1 1210 1210 D10 D10 . L 7 D10 A 1 1211 1211 D10 D10 . M 7 D10 A 1 1212 1212 D10 D10 . N 7 D10 A 1 1213 1213 D10 D10 . O 7 D10 A 1 1214 1214 D10 D10 . P 8 C14 A 1 1215 1215 C14 C14 . Q 9 D12 A 1 1216 1216 D12 D12 . R 7 D10 A 1 1217 1217 D10 D10 . S 7 D10 A 1 1218 1218 D10 D10 . T 7 D10 A 1 1219 1219 D10 D10 . U 6 CLR A 1 1220 1220 CLR CLR . V 6 CLR A 1 1221 1221 CLR CLR . W 10 NAG A 1 1222 1222 NAG NAG . X 11 SPK A 1 1223 1223 SPK SPK . Y 12 EUJ A 1 1224 1224 EUJ EUJ . Z 13 HOH A 1 1301 1301 HOH HOH . Z 13 HOH A 2 1302 1302 HOH HOH . Z 13 HOH A 3 1303 1303 HOH HOH . Z 13 HOH A 4 1304 1304 HOH HOH . Z 13 HOH A 5 1305 1305 HOH HOH . Z 13 HOH A 6 1306 1306 HOH HOH . Z 13 HOH A 7 1307 1307 HOH HOH . Z 13 HOH A 8 1308 1308 HOH HOH . # 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 SPK . . . X 11 165.048 161.279 177.661 1 83.83 ? N1 SPK 1223 A 1 HETATM 2 C C2 SPK . . . X 11 165.63 162.672 177.65 1 83.83 ? C2 SPK 1223 A 1 HETATM 3 C C3 SPK . . . X 11 165.757 163.142 179.102 1 83.83 ? C3 SPK 1223 A 1 HETATM 4 C C4 SPK . . . X 11 167.2 163.349 179.488 1 83.83 ? C4 SPK 1223 A 1 HETATM 5 N N5 SPK . . . X 11 167.257 164.013 180.843 1 83.83 ? N5 SPK 1223 A 1 HETATM 6 C C6 SPK . . . X 11 168.7 164.017 181.272 1 83.83 ? C6 SPK 1223 A 1 HETATM 7 C C7 SPK . . . X 11 168.731 164.869 182.515 1 83.83 ? C7 SPK 1223 A 1 HETATM 8 C C8 SPK . . . X 11 170.15 164.768 183.011 1 83.83 ? C8 SPK 1223 A 1 HETATM 9 C C9 SPK . . . X 11 170.141 165.607 184.269 1 83.83 ? C9 SPK 1223 A 1 HETATM 10 N N10 SPK . . . X 11 171.584 165.658 184.7 1 83.83 ? N10 SPK 1223 A 1 HETATM 11 C C11 SPK . . . X 11 171.714 166.64 185.837 1 83.83 ? C11 SPK 1223 A 1 HETATM 12 C C12 SPK . . . X 11 173.207 166.86 186 1 83.83 ? C12 SPK 1223 A 1 HETATM 13 C C13 SPK . . . X 11 173.398 167.937 187.048 1 83.83 ? C13 SPK 1223 A 1 HETATM 14 N N14 SPK . . . X 11 174.813 168.489 186.919 1 83.83 ? N14 SPK 1223 A 1 HETATM 15 H H1A SPK . . . X 11 165.58 160.657 178.294 1 83.83 ? H1A SPK 1223 A 1 HETATM 16 H H1B SPK . . . X 11 164.063 161.303 177.978 1 83.83 ? H1B SPK 1223 A 1 HETATM 17 H H1C SPK . . . X 11 165.069 160.867 176.712 1 83.83 ? H1C SPK 1223 A 1 HETATM 18 H H2A SPK . . . X 11 164.985 163.351 177.037 1 83.83 ? H2A SPK 1223 A 1 HETATM 19 H H2B SPK . . . X 11 166.616 162.645 177.12 1 83.83 ? H2B SPK 1223 A 1 HETATM 20 H H3A SPK . . . X 11 165.361 162.403 179.834 1 83.83 ? H3A SPK 1223 A 1 HETATM 21 H H3B SPK . . . X 11 165.163 164.062 179.286 1 83.83 ? H3B SPK 1223 A 1 HETATM 22 H H4A SPK . . . X 11 167.731 164 178.742 1 83.83 ? H4A SPK 1223 A 1 HETATM 23 H H4B SPK . . . X 11 167.79 162.399 179.527 1 83.83 ? H4B SPK 1223 A 1 HETATM 24 H H5A SPK . . . X 11 166.698 163.496 181.554 1 83.83 ? H5A SPK 1223 A 1 HETATM 25 H H5B SPK . . . X 11 166.892 164.981 180.836 1 83.83 ? H5B SPK 1223 A 1 HETATM 26 H H6A SPK . . . X 11 169.049 162.967 181.466 1 83.83 ? H6A SPK 1223 A 1 HETATM 27 H H6B SPK . . . X 11 169.359 164.406 180.463 1 83.83 ? H6B SPK 1223 A 1 HETATM 28 H H7A SPK . . . X 11 168.007 164.516 183.286 1 83.83 ? H7A SPK 1223 A 1 HETATM 29 H H7B SPK . . . X 11 168.432 165.923 182.322 1 83.83 ? H7B SPK 1223 A 1 HETATM 30 H H8A SPK . . . X 11 170.896 165.143 182.272 1 83.83 ? H8A SPK 1223 A 1 HETATM 31 H H8B SPK . . . X 11 170.443 163.707 183.19 1 83.83 ? H8B SPK 1223 A 1 HETATM 32 H H9A SPK . . . X 11 169.49 165.164 185.068 1 83.83 ? H9A SPK 1223 A 1 HETATM 33 H H9B SPK . . . X 11 169.731 166.625 184.113 1 83.83 ? H9B SPK 1223 A 1 HETATM 34 H H101 SPK . . . X 11 172.201 165.925 183.899 1 83.83 ? H101 SPK 1223 A 1 HETATM 35 H H102 SPK . . . X 11 171.888 164.71 184.985 1 83.83 ? H102 SPK 1223 A 1 HETATM 36 H H111 SPK . . . X 11 171.214 166.221 186.75 1 83.83 ? H111 SPK 1223 A 1 HETATM 37 H H112 SPK . . . X 11 171.142 167.572 185.61 1 83.83 ? H112 SPK 1223 A 1 HETATM 38 H H121 SPK . . . X 11 173.674 167.186 185.037 1 83.83 ? H121 SPK 1223 A 1 HETATM 39 H H122 SPK . . . X 11 173.733 165.906 186.229 1 83.83 ? H122 SPK 1223 A 1 HETATM 40 H H131 SPK . . . X 11 173.219 167.523 188.066 1 83.83 ? H131 SPK 1223 A 1 HETATM 41 H H132 SPK . . . X 11 172.647 168.761 186.929 1 83.83 ? H132 SPK 1223 A 1 HETATM 42 H H141 SPK . . . X 11 174.952 169.291 187.556 1 83.83 ? H141 SPK 1223 A 1 HETATM 43 H H142 SPK . . . X 11 175.011 168.819 185.961 1 83.83 ? H142 SPK 1223 A 1 HETATM 44 H H143 SPK . . . X 11 175.515 167.764 187.144 1 83.83 ? H143 SPK 1223 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 27 _model_server_stats.query_time_ms 317 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 44 #