data_3P4J
#
_model_server_result.job_id            Ag4FfqTMuueeu6PZ2b305g 
_model_server_result.datetime_utc      '2025-01-10 11:32:13' 
_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          3p4j 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":20}' 
#
_entry.id    3P4J 
#
_exptl.entry_id    3P4J 
_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    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            3P4J 
_cell.length_a            17.88 
_cell.length_b            31.42 
_cell.length_c            43.9 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 3P4J 
_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    dimeric 
_pdbx_struct_assembly.oligomeric_count      2 
_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 
_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                      2 
_struct_asym.id                             C 
_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
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                     3P4J 
_atom_sites.fract_transf_matrix[1][1]    0.055928 
_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]    0.031827 
_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]    0.022779 
_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 20 20 SPM SPM . 
D 3 HOH A 1 103 103 HOH HOH . 
D 3 HOH A 2 107 107 HOH HOH . 
D 3 HOH A 3 109 109 HOH HOH . 
D 3 HOH A 4 111 111 HOH HOH . 
D 3 HOH A 5 112 112 HOH HOH . 
D 3 HOH A 6 113 113 HOH HOH . 
D 3 HOH A 7 115 115 HOH HOH . 
D 3 HOH A 8 122 122 HOH HOH . 
D 3 HOH A 9 123 123 HOH HOH . 
D 3 HOH A 10 132 132 HOH HOH . 
D 3 HOH A 11 134 134 HOH HOH . 
D 3 HOH A 12 135 135 HOH HOH . 
D 3 HOH A 13 136 136 HOH HOH . 
D 3 HOH A 14 137 137 HOH HOH . 
D 3 HOH A 15 140 140 HOH HOH . 
D 3 HOH A 16 142 142 HOH HOH . 
D 3 HOH A 17 147 147 HOH HOH . 
D 3 HOH A 18 148 148 HOH HOH . 
D 3 HOH A 19 149 149 HOH HOH . 
D 3 HOH A 20 152 152 HOH HOH . 
D 3 HOH A 21 153 153 HOH HOH . 
D 3 HOH A 22 158 158 HOH HOH . 
D 3 HOH A 23 159 159 HOH HOH . 
D 3 HOH A 24 160 160 HOH HOH . 
D 3 HOH A 25 162 162 HOH HOH . 
D 3 HOH A 26 163 163 HOH HOH . 
D 3 HOH A 27 166 166 HOH HOH . 
D 3 HOH A 28 167 167 HOH HOH . 
D 3 HOH A 29 170 170 HOH HOH . 
D 3 HOH A 30 171 171 HOH HOH . 
D 3 HOH A 31 175 175 HOH HOH . 
D 3 HOH A 32 176 176 HOH HOH . 
D 3 HOH A 33 178 178 HOH HOH . 
D 3 HOH A 34 179 179 HOH HOH . 
D 3 HOH A 35 184 184 HOH HOH . 
D 3 HOH A 36 185 185 HOH HOH . 
D 3 HOH A 37 186 186 HOH HOH . 
D 3 HOH A 38 187 187 HOH HOH . 
D 3 HOH A 39 189 189 HOH HOH . 
D 3 HOH A 40 191 191 HOH HOH . 
D 3 HOH A 41 195 195 HOH HOH . 
D 3 HOH A 42 196 196 HOH HOH . 
D 3 HOH A 43 197 197 HOH HOH . 
D 3 HOH A 44 199 199 HOH HOH . 
D 3 HOH A 45 201 201 HOH HOH . 
D 3 HOH A 46 202 202 HOH HOH . 
D 3 HOH A 47 205 205 HOH HOH . 
D 3 HOH A 48 206 206 HOH HOH . 
D 3 HOH A 49 207 207 HOH HOH . 
D 3 HOH A 50 208 208 HOH HOH . 
D 3 HOH A 51 210 210 HOH HOH . 
D 3 HOH A 52 219 219 HOH HOH . 
D 3 HOH A 53 220 220 HOH HOH . 
D 3 HOH A 54 221 221 HOH HOH . 
D 3 HOH A 55 222 222 HOH HOH . 
D 3 HOH A 56 224 224 HOH HOH . 
D 3 HOH A 57 225 225 HOH HOH . 
D 3 HOH A 58 226 226 HOH HOH . 
D 3 HOH A 59 229 229 HOH HOH . 
D 3 HOH A 60 230 230 HOH HOH . 
D 3 HOH A 61 231 231 HOH HOH . 
D 3 HOH A 62 232 232 HOH HOH . 
D 3 HOH A 63 233 233 HOH HOH . 
E 3 HOH B 1 101 101 HOH HOH . 
E 3 HOH B 2 102 102 HOH HOH . 
E 3 HOH B 3 104 104 HOH HOH . 
E 3 HOH B 4 105 105 HOH HOH . 
E 3 HOH B 5 106 106 HOH HOH . 
E 3 HOH B 6 108 108 HOH HOH . 
E 3 HOH B 7 110 110 HOH HOH . 
E 3 HOH B 8 114 114 HOH HOH . 
E 3 HOH B 9 116 116 HOH HOH . 
E 3 HOH B 10 117 117 HOH HOH . 
E 3 HOH B 11 118 118 HOH HOH . 
E 3 HOH B 12 119 119 HOH HOH . 
E 3 HOH B 13 120 120 HOH HOH . 
E 3 HOH B 14 121 121 HOH HOH . 
E 3 HOH B 15 124 124 HOH HOH . 
E 3 HOH B 16 125 125 HOH HOH . 
E 3 HOH B 17 126 126 HOH HOH . 
E 3 HOH B 18 127 127 HOH HOH . 
E 3 HOH B 19 128 128 HOH HOH . 
E 3 HOH B 20 129 129 HOH HOH . 
E 3 HOH B 21 130 130 HOH HOH . 
E 3 HOH B 22 131 131 HOH HOH . 
E 3 HOH B 23 133 133 HOH HOH . 
E 3 HOH B 24 138 138 HOH HOH . 
E 3 HOH B 25 139 139 HOH HOH . 
E 3 HOH B 26 141 141 HOH HOH . 
E 3 HOH B 27 144 144 HOH HOH . 
E 3 HOH B 28 145 145 HOH HOH . 
E 3 HOH B 29 146 146 HOH HOH . 
E 3 HOH B 30 150 150 HOH HOH . 
E 3 HOH B 31 151 151 HOH HOH . 
E 3 HOH B 32 154 154 HOH HOH . 
E 3 HOH B 33 155 155 HOH HOH . 
E 3 HOH B 34 156 156 HOH HOH . 
E 3 HOH B 35 157 157 HOH HOH . 
E 3 HOH B 36 161 161 HOH HOH . 
E 3 HOH B 37 164 164 HOH HOH . 
E 3 HOH B 38 165 165 HOH HOH . 
E 3 HOH B 39 168 168 HOH HOH . 
E 3 HOH B 40 169 169 HOH HOH . 
E 3 HOH B 41 172 172 HOH HOH . 
E 3 HOH B 42 173 173 HOH HOH . 
E 3 HOH B 43 174 174 HOH HOH . 
E 3 HOH B 44 177 177 HOH HOH . 
E 3 HOH B 45 180 180 HOH HOH . 
E 3 HOH B 46 181 181 HOH HOH . 
E 3 HOH B 47 182 182 HOH HOH . 
E 3 HOH B 48 183 183 HOH HOH . 
E 3 HOH B 49 188 188 HOH HOH . 
E 3 HOH B 50 190 190 HOH HOH . 
E 3 HOH B 51 192 192 HOH HOH . 
E 3 HOH B 52 193 193 HOH HOH . 
E 3 HOH B 53 194 194 HOH HOH . 
E 3 HOH B 54 198 198 HOH HOH . 
E 3 HOH B 55 200 200 HOH HOH . 
E 3 HOH B 56 203 203 HOH HOH . 
E 3 HOH B 57 204 204 HOH HOH . 
E 3 HOH B 58 209 209 HOH HOH . 
E 3 HOH B 59 212 212 HOH HOH . 
E 3 HOH B 60 214 214 HOH HOH . 
E 3 HOH B 61 217 217 HOH HOH . 
E 3 HOH B 62 218 218 HOH HOH . 
E 3 HOH B 63 228 228 HOH HOH . 
E 3 HOH B 64 234 234 HOH HOH . 
E 3 HOH B 65 235 235 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 7.303 7.739 32.241 1 2.54 ? N1 SPM 20 A 1 
HETATM 2 C C2 SPM . . . C 2 7.995 6.935 31.211 1 2.8 ? C2 SPM 20 A 1 
HETATM 3 C C3 SPM . . . C 2 9.416 7.461 31.007 1 3.54 ? C3 SPM 20 A 1 
HETATM 4 C C4 SPM . . . C 2 10.267 6.637 30.043 1 4.06 ? C4 SPM 20 A 1 
HETATM 5 N N5 SPM . . . C 2 10.779 5.398 30.645 1 4.54 ? N5 SPM 20 A 1 
HETATM 6 C C6 SPM . . . C 2 11.674 4.627 29.772 1 5.55 ? C6 SPM 20 A 1 
HETATM 7 C C7 SPM . A . C 2 11.756 3.188 30.282 0.56 8.28 ? C7 SPM 20 A 1 
HETATM 8 C C7 SPM . B . C 2 12.464 3.548 30.516 0.44 6.09 ? C7 SPM 20 A 1 
HETATM 9 C C8 SPM . A . C 2 13.175 2.774 30.663 0.56 12.23 ? C8 SPM 20 A 1 
HETATM 10 C C8 SPM . B . C 2 11.67 2.323 30.952 0.44 5.38 ? C8 SPM 20 A 1 
HETATM 11 C C9 SPM . A . C 2 13.199 1.356 31.238 0.56 11.99 ? C9 SPM 20 A 1 
HETATM 12 C C9 SPM . B . C 2 12.526 1.218 31.566 0.44 6.97 ? C9 SPM 20 A 1 
HETATM 13 N N10 SPM . A . C 2 13.254 1.392 32.707 0.56 6.53 ? N10 SPM 20 A 1 
HETATM 14 N N10 SPM . B . C 2 12.924 1.556 32.94 0.44 8.75 ? N10 SPM 20 A 1 
HETATM 15 C C11 SPM . A . C 2 13.514 0.044 33.233 0.56 7.84 ? C11 SPM 20 A 1 
HETATM 16 C C11 SPM . B . C 2 13.287 0.324 33.658 0.44 13.72 ? C11 SPM 20 A 1 
HETATM 17 C C12 SPM . A . C 2 14.13 0.148 34.63 0.56 15.91 ? C12 SPM 20 A 1 
HETATM 18 C C12 SPM . B . C 2 13.802 0.675 35.056 0.44 15.23 ? C12 SPM 20 A 1 
HETATM 19 C C13 SPM . A . C 2 13.413 1.217 35.46 0.56 17.69 ? C13 SPM 20 A 1 
HETATM 20 C C13 SPM . B . C 2 14.041 -0.593 35.879 0.44 16.76 ? C13 SPM 20 A 1 
HETATM 21 N N14 SPM . A . C 2 13.477 0.851 36.883 0.56 24.77 ? N14 SPM 20 A 1 
HETATM 22 N N14 SPM . B . C 2 13.021 -0.693 36.933 0.44 14.36 ? N14 SPM 20 A 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           306 
_model_server_stats.encode_time_ms          6 
_model_server_stats.element_count           22 
#