data_131D # _model_server_result.job_id c7RQBo8y2G39mJvHJi-00A _model_server_result.datetime_utc '2024-10-18 12:33:30' _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 131d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":13}' # _entry.id 131D # _exptl.entry_id 131D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 202.34 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description SPERMINE _entity.pdbx_number_of_molecules 2 _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 131D _cell.length_a 18.265 _cell.length_b 30.69 _cell.length_c 42.46 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 131D _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 ? _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 ? 2 C N N ? 2 F N 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 O3' DG 4 A DG 4 1_555 E NA NA . A NA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.844 ? metalc ? metalc2 A OP1 DC 5 A DC 5 1_555 D NA NA . A NA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.66 ? metalc ? metalc3 A OP1 DC 5 A DC 5 1_555 E NA NA . A NA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.984 ? metalc ? metalc4 A OP2 DC 5 A DC 5 1_555 E NA NA . A NA 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.804 ? metalc ? metalc5 D NA NA . A NA 15 1_555 G O HOH . A HOH 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? metalc ? metalc6 D NA NA . A NA 15 1_555 G O HOH . A HOH 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.757 ? metalc ? metalc7 D NA NA . A NA 15 1_555 G O HOH . A HOH 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.984 ? metalc ? metalc8 D NA NA . A NA 15 1_555 G O HOH . A HOH 21 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.902 ? metalc ? metalc9 E NA NA . A NA 16 1_555 G O HOH . A HOH 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.794 ? metalc ? metalc10 E NA NA . A NA 16 1_555 G O HOH . A HOH 22 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.809 ? metalc ? metalc11 E NA NA . A NA 16 1_555 G O HOH . A HOH 23 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.607 ? metalc ? metalc12 E NA NA . A NA 16 1_555 G O HOH . A HOH 24 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.75 ? hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 6 B DG 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 5 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog7 A N3 DC 3 A DC 3 1_555 B N1 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog8 A N4 DC 3 A DC 3 1_555 B O6 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog9 A O2 DC 3 A DC 3 1_555 B N2 DG 4 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 3 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog13 A N3 DC 5 A DC 5 1_555 B N1 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog14 A N4 DC 5 A DC 5 1_555 B O6 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog15 A O2 DC 5 A DC 5 1_555 B N2 DG 2 B DG 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog16 A N1 DG 6 A DG 6 1_555 B N3 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog17 A N2 DG 6 A DG 6 1_555 B O2 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? hydrog WATSON-CRICK hydrog18 A O6 DG 6 A DG 6 1_555 B N4 DC 1 B DC 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? # _chem_comp.formula 'C10 H26 N4' _chem_comp.formula_weight 202.34 _chem_comp.id SPM _chem_comp.mon_nstd_flag . _chem_comp.name SPERMINE _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 SPM sing 77 n n N1 HN11 SPM sing 78 n n N1 HN12 SPM sing 79 n n C2 C3 SPM sing 80 n n C2 H21 SPM sing 81 n n C2 H22 SPM sing 82 n n C3 C4 SPM sing 83 n n C3 H31 SPM sing 84 n n C3 H32 SPM sing 85 n n C4 N5 SPM sing 86 n n C4 H41 SPM sing 87 n n C4 H42 SPM sing 88 n n N5 C6 SPM sing 89 n n N5 HN5 SPM sing 90 n n C6 C7 SPM sing 91 n n C6 H61 SPM sing 92 n n C6 H62 SPM sing 93 n n C7 C8 SPM sing 94 n n C7 H71 SPM sing 95 n n C7 H72 SPM sing 96 n n C8 C9 SPM sing 97 n n C8 H81 SPM sing 98 n n C8 H82 SPM sing 99 n n C9 N10 SPM sing 100 n n C9 H91 SPM sing 101 n n C9 H92 SPM sing 102 n n N10 C11 SPM sing 103 n n N10 HN0 SPM sing 104 n n C11 C12 SPM sing 105 n n C11 H111 SPM sing 106 n n C11 H112 SPM sing 107 n n C12 C13 SPM sing 108 n n C12 H121 SPM sing 109 n n C12 H122 SPM sing 110 n n C13 N14 SPM sing 111 n n C13 H131 SPM sing 112 n n C13 H132 SPM sing 113 n n N14 HN41 SPM sing 114 n n N14 HN42 SPM sing 115 n n # _atom_sites.entry_id 131D _atom_sites.fract_transf_matrix[1][1] 0.05475 _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] 0.032584 _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] 0.023552 _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 C 2 SPM A 1 13 13 SPM SPM . D 3 NA A 1 15 15 NA NA . E 3 NA A 1 16 16 NA NA . F 2 SPM B 1 14 14 SPM SPM . G 4 HOH A 1 17 17 HOH HOH . G 4 HOH A 2 18 18 HOH HOH . G 4 HOH A 3 19 19 HOH HOH . G 4 HOH A 4 20 20 HOH HOH . G 4 HOH A 5 21 21 HOH HOH . G 4 HOH A 6 22 22 HOH HOH . G 4 HOH A 7 23 23 HOH HOH . G 4 HOH A 8 24 24 HOH HOH . G 4 HOH A 9 25 25 HOH HOH . G 4 HOH A 10 27 27 HOH HOH . G 4 HOH A 11 28 28 HOH HOH . G 4 HOH A 12 31 31 HOH HOH . G 4 HOH A 13 32 32 HOH HOH . G 4 HOH A 14 35 35 HOH HOH . G 4 HOH A 15 36 36 HOH HOH . G 4 HOH A 16 37 37 HOH HOH . G 4 HOH A 17 39 39 HOH HOH . G 4 HOH A 18 42 42 HOH HOH . G 4 HOH A 19 44 44 HOH HOH . G 4 HOH A 20 45 45 HOH HOH . G 4 HOH A 21 46 46 HOH HOH . G 4 HOH A 22 47 47 HOH HOH . G 4 HOH A 23 55 55 HOH HOH . G 4 HOH A 24 58 58 HOH HOH . G 4 HOH A 25 59 59 HOH HOH . G 4 HOH A 26 60 60 HOH HOH . G 4 HOH A 27 62 62 HOH HOH . G 4 HOH A 28 64 64 HOH HOH . G 4 HOH A 29 65 65 HOH HOH . G 4 HOH A 30 66 66 HOH HOH . G 4 HOH A 31 67 67 HOH HOH . G 4 HOH A 32 68 68 HOH HOH . G 4 HOH A 33 69 69 HOH HOH . G 4 HOH A 34 70 70 HOH HOH . G 4 HOH A 35 71 71 HOH HOH . G 4 HOH A 36 72 72 HOH HOH . G 4 HOH A 37 73 73 HOH HOH . G 4 HOH A 38 74 74 HOH HOH . H 4 HOH B 1 26 26 HOH HOH . H 4 HOH B 2 29 29 HOH HOH . H 4 HOH B 3 30 30 HOH HOH . H 4 HOH B 4 33 33 HOH HOH . H 4 HOH B 5 34 34 HOH HOH . H 4 HOH B 6 38 38 HOH HOH . H 4 HOH B 7 40 40 HOH HOH . H 4 HOH B 8 41 41 HOH HOH . H 4 HOH B 9 43 43 HOH HOH . H 4 HOH B 10 48 48 HOH HOH . H 4 HOH B 11 49 49 HOH HOH . H 4 HOH B 12 50 50 HOH HOH . H 4 HOH B 13 51 51 HOH HOH . H 4 HOH B 14 52 52 HOH HOH . H 4 HOH B 15 53 53 HOH HOH . H 4 HOH B 16 54 54 HOH HOH . H 4 HOH B 17 56 56 HOH HOH . H 4 HOH B 18 57 57 HOH HOH . H 4 HOH B 19 61 61 HOH HOH . H 4 HOH B 20 63 63 HOH HOH . H 4 HOH B 21 75 75 HOH HOH . H 4 HOH B 22 76 76 HOH HOH . H 4 HOH B 23 77 77 HOH HOH . H 4 HOH B 24 78 78 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 SPM . . . C 2 23.536 18.439 26.873 1 7.2 ? N1 SPM 13 A 1 HETATM 2 C C2 SPM . . . C 2 23.455 17.02 26.268 1 7.06 ? C2 SPM 13 A 1 HETATM 3 C C3 SPM . . . C 2 22.24 17.003 25.351 1 7.51 ? C3 SPM 13 A 1 HETATM 4 C C4 SPM . . . C 2 21.893 15.53 24.867 1 8.62 ? C4 SPM 13 A 1 HETATM 5 N N5 SPM . . . C 2 23.049 15.019 23.967 1 8.89 ? N5 SPM 13 A 1 HETATM 6 C C6 SPM . . . C 2 22.416 13.743 23.242 1 9.65 ? C6 SPM 13 A 1 HETATM 7 C C7 SPM . . . C 2 23.495 13.119 22.383 1 11.09 ? C7 SPM 13 A 1 HETATM 8 C C8 SPM . . . C 2 22.92 12.276 21.221 1 10.02 ? C8 SPM 13 A 1 HETATM 9 C C9 SPM . . . C 2 24.082 11.795 20.369 1 11.33 ? C9 SPM 13 A 1 HETATM 10 N N10 SPM . . . C 2 23.509 10.751 19.354 1 10.86 ? N10 SPM 13 A 1 HETATM 11 C C11 SPM . . . C 2 24.709 10.317 18.441 1 12.77 ? C11 SPM 13 A 1 HETATM 12 C C12 SPM . . . C 2 24.031 9.361 17.322 1 12.36 ? C12 SPM 13 A 1 HETATM 13 C C13 SPM . . . C 2 25.221 8.811 16.488 1 12.94 ? C13 SPM 13 A 1 HETATM 14 N N14 SPM . . . C 2 24.826 7.81 15.432 1 11.66 ? N14 SPM 13 A 1 # _model_server_stats.io_time_ms 114 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 1 _model_server_stats.query_time_ms 270 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 14 #