data_2RF3
#
_model_server_result.job_id            TTy574D-fzCILTS9akEGsg 
_model_server_result.datetime_utc      '2025-04-20 20:13:11' 
_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          2rf3 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":309}' 
#
_entry.id    2RF3 
#
_exptl.entry_id    2RF3 
_exptl.method      'X-RAY DIFFRACTION' 
#
_entity.details                     ? 
_entity.formula_weight              202.34 
_entity.id                          3 
_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         120 
_cell.entry_id            2RF3 
_cell.length_a            26.587 
_cell.length_b            26.587 
_cell.length_c            98.238 
_cell.Z_PDB               6 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 2RF3 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        145 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 32' 
#
_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,F 
_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                      3 
_struct_asym.id                             D 
_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 O3' DG 4 A DG 4 1_555 A P TCY 5 A TCY 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.588 ? 
covale ? covale2 A O3' TCY 5 A TCY 5 1_555 A P DA 6 A DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.576 ? 
covale ? covale3 B O3' DG 4 B DG 4 1_555 B P TCY 5 B TCY 5 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.588 ? 
covale ? covale4 B O3' TCY 5 B TCY 5 1_555 B P DA 6 B DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.578 ? 
metalc ? metalc1 B OP1 DG 12 B DG 12 1_555 C ZN ZN . B ZN 308 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? 
hydrog WATSON-CRICK hydrog1 A N1 DG 2 A DG 2 1_555 B N3 DC 11 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N2 DG 2 A DG 2 1_555 B O2 DC 11 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O6 DG 2 A DG 2 1_555 B N4 DC 11 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N3 DC 3 A DC 3 1_555 B N1 DG 10 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N4 DC 3 A DC 3 1_555 B O6 DG 10 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O2 DC 3 A DC 3 1_555 B N2 DG 10 B DG 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N1 DG 4 A DG 4 1_555 B N3 DC 9 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N2 DG 4 A DG 4 1_555 B O2 DC 9 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A O6 DG 4 A DG 4 1_555 B N4 DC 9 B DC 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N1 DA 6 A DA 6 1_555 B N3 DT 7 B DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N6 DA 6 A DA 6 1_555 B O4 DT 7 B DT 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A N3 DT 7 A DT 7 1_555 B N1 DA 6 B DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A O4 DT 7 A DT 7 1_555 B N6 DA 6 B DA 6 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N3 DC 9 A DC 9 1_555 B N1 DG 4 B DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A N4 DC 9 A DC 9 1_555 B O6 DG 4 B DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A O2 DC 9 A DC 9 1_555 B N2 DG 4 B DG 4 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A N1 DG 10 A DG 10 1_555 B N3 DC 3 B DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A N2 DG 10 A DG 10 1_555 B O2 DC 3 B DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog19 A O6 DG 10 A DG 10 1_555 B N4 DC 3 B DC 3 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog20 A N3 DC 11 A DC 11 1_555 B N1 DG 2 B DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog21 A N4 DC 11 A DC 11 1_555 B O6 DG 2 B DG 2 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog22 A O2 DC 11 A DC 11 1_555 B N2 DG 2 B DG 2 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 152 n n 
N1 HN11 SPM sing 153 n n 
N1 HN12 SPM sing 154 n n 
C2 C3 SPM sing 155 n n 
C2 H21 SPM sing 156 n n 
C2 H22 SPM sing 157 n n 
C3 C4 SPM sing 158 n n 
C3 H31 SPM sing 159 n n 
C3 H32 SPM sing 160 n n 
C4 N5 SPM sing 161 n n 
C4 H41 SPM sing 162 n n 
C4 H42 SPM sing 163 n n 
N5 C6 SPM sing 164 n n 
N5 HN5 SPM sing 165 n n 
C6 C7 SPM sing 166 n n 
C6 H61 SPM sing 167 n n 
C6 H62 SPM sing 168 n n 
C7 C8 SPM sing 169 n n 
C7 H71 SPM sing 170 n n 
C7 H72 SPM sing 171 n n 
C8 C9 SPM sing 172 n n 
C8 H81 SPM sing 173 n n 
C8 H82 SPM sing 174 n n 
C9 N10 SPM sing 175 n n 
C9 H91 SPM sing 176 n n 
C9 H92 SPM sing 177 n n 
N10 C11 SPM sing 178 n n 
N10 HN0 SPM sing 179 n n 
C11 C12 SPM sing 180 n n 
C11 H111 SPM sing 181 n n 
C11 H112 SPM sing 182 n n 
C12 C13 SPM sing 183 n n 
C12 H121 SPM sing 184 n n 
C12 H122 SPM sing 185 n n 
C13 N14 SPM sing 186 n n 
C13 H131 SPM sing 187 n n 
C13 H132 SPM sing 188 n n 
N14 HN41 SPM sing 189 n n 
N14 HN42 SPM sing 190 n n 
#
_atom_sites.entry_id                     2RF3 
_atom_sites.fract_transf_matrix[1][1]    0.037612 
_atom_sites.fract_transf_matrix[1][2]    0.021716 
_atom_sites.fract_transf_matrix[1][3]    0 
_atom_sites.fract_transf_matrix[2][1]    0 
_atom_sites.fract_transf_matrix[2][2]    0.043431 
_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]    0.010179 
_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 ZN B 1 308 308 ZN ZN . 
D 3 SPM B 1 309 309 SPM SPM . 
E 4 HOH A 1 209 209 HOH HOH . 
E 4 HOH A 2 210 210 HOH HOH . 
E 4 HOH A 3 218 218 HOH HOH . 
E 4 HOH A 4 219 219 HOH HOH . 
E 4 HOH A 5 220 220 HOH HOH . 
E 4 HOH A 6 221 221 HOH HOH . 
E 4 HOH A 7 224 224 HOH HOH . 
E 4 HOH A 8 225 225 HOH HOH . 
E 4 HOH A 9 226 226 HOH HOH . 
E 4 HOH A 10 227 227 HOH HOH . 
E 4 HOH A 11 228 228 HOH HOH . 
E 4 HOH A 12 229 229 HOH HOH . 
E 4 HOH A 13 233 233 HOH HOH . 
E 4 HOH A 14 234 234 HOH HOH . 
E 4 HOH A 15 235 235 HOH HOH . 
E 4 HOH A 16 239 239 HOH HOH . 
E 4 HOH A 17 240 240 HOH HOH . 
E 4 HOH A 18 243 243 HOH HOH . 
E 4 HOH A 19 244 244 HOH HOH . 
E 4 HOH A 20 245 245 HOH HOH . 
E 4 HOH A 21 246 246 HOH HOH . 
E 4 HOH A 22 247 247 HOH HOH . 
E 4 HOH A 23 262 262 HOH HOH . 
E 4 HOH A 24 263 263 HOH HOH . 
E 4 HOH A 25 264 264 HOH HOH . 
E 4 HOH A 26 265 265 HOH HOH . 
E 4 HOH A 27 268 268 HOH HOH . 
E 4 HOH A 28 269 269 HOH HOH . 
E 4 HOH A 29 270 270 HOH HOH . 
E 4 HOH A 30 271 271 HOH HOH . 
E 4 HOH A 31 272 272 HOH HOH . 
E 4 HOH A 32 273 273 HOH HOH . 
E 4 HOH A 33 274 274 HOH HOH . 
E 4 HOH A 34 275 275 HOH HOH . 
E 4 HOH A 35 276 276 HOH HOH . 
E 4 HOH A 36 277 277 HOH HOH . 
E 4 HOH A 37 279 279 HOH HOH . 
E 4 HOH A 38 289 289 HOH HOH . 
E 4 HOH A 39 290 290 HOH HOH . 
E 4 HOH A 40 296 296 HOH HOH . 
E 4 HOH A 41 297 297 HOH HOH . 
E 4 HOH A 42 299 299 HOH HOH . 
E 4 HOH A 43 301 301 HOH HOH . 
E 4 HOH A 44 302 302 HOH HOH . 
E 4 HOH A 45 303 303 HOH HOH . 
F 4 HOH B 1 201 201 HOH HOH . 
F 4 HOH B 2 203 203 HOH HOH . 
F 4 HOH B 3 204 204 HOH HOH . 
F 4 HOH B 4 205 205 HOH HOH . 
F 4 HOH B 5 206 206 HOH HOH . 
F 4 HOH B 6 207 207 HOH HOH . 
F 4 HOH B 7 208 208 HOH HOH . 
F 4 HOH B 8 211 211 HOH HOH . 
F 4 HOH B 9 212 212 HOH HOH . 
F 4 HOH B 10 213 213 HOH HOH . 
F 4 HOH B 11 214 214 HOH HOH . 
F 4 HOH B 12 215 215 HOH HOH . 
F 4 HOH B 13 216 216 HOH HOH . 
F 4 HOH B 14 217 217 HOH HOH . 
F 4 HOH B 15 222 222 HOH HOH . 
F 4 HOH B 16 223 223 HOH HOH . 
F 4 HOH B 17 231 231 HOH HOH . 
F 4 HOH B 18 232 232 HOH HOH . 
F 4 HOH B 19 236 236 HOH HOH . 
F 4 HOH B 20 237 237 HOH HOH . 
F 4 HOH B 21 238 238 HOH HOH . 
F 4 HOH B 22 241 241 HOH HOH . 
F 4 HOH B 23 242 242 HOH HOH . 
F 4 HOH B 24 249 249 HOH HOH . 
F 4 HOH B 25 251 251 HOH HOH . 
F 4 HOH B 26 252 252 HOH HOH . 
F 4 HOH B 27 253 253 HOH HOH . 
F 4 HOH B 28 254 254 HOH HOH . 
F 4 HOH B 29 255 255 HOH HOH . 
F 4 HOH B 30 256 256 HOH HOH . 
F 4 HOH B 31 257 257 HOH HOH . 
F 4 HOH B 32 259 259 HOH HOH . 
F 4 HOH B 33 260 260 HOH HOH . 
F 4 HOH B 34 266 266 HOH HOH . 
F 4 HOH B 35 278 278 HOH HOH . 
F 4 HOH B 36 281 281 HOH HOH . 
F 4 HOH B 37 285 285 HOH HOH . 
F 4 HOH B 38 286 286 HOH HOH . 
F 4 HOH B 39 288 288 HOH HOH . 
F 4 HOH B 40 291 291 HOH HOH . 
F 4 HOH B 41 292 292 HOH HOH . 
F 4 HOH B 42 293 293 HOH HOH . 
F 4 HOH B 43 294 294 HOH HOH . 
F 4 HOH B 44 298 298 HOH HOH . 
F 4 HOH B 45 304 304 HOH HOH . 
F 4 HOH B 46 305 305 HOH HOH . 
F 4 HOH B 47 306 306 HOH HOH . 
F 4 HOH B 48 307 307 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 . . . D 3 9.128 12.977 13.475 1 41.93 ? N1 SPM 309 B 1 
HETATM 2 C C2 SPM . . . D 3 9.527 11.953 12.523 1 41.24 ? C2 SPM 309 B 1 
HETATM 3 C C3 SPM . . . D 3 10.748 11.211 13.062 1 40.09 ? C3 SPM 309 B 1 
HETATM 4 C C4 SPM . . . D 3 10.363 10.024 13.939 1 39.14 ? C4 SPM 309 B 1 
HETATM 5 N N5 SPM . . . D 3 11.543 9.377 14.478 1 38.47 ? N5 SPM 309 B 1 
HETATM 6 C C6 SPM . . . D 3 12.221 9.972 15.609 1 37.64 ? C6 SPM 309 B 1 
HETATM 7 C C7 SPM . . . D 3 13.477 9.215 15.999 1 36.19 ? C7 SPM 309 B 1 
HETATM 8 C C8 SPM . . . D 3 14.264 9.991 17.03 1 37.45 ? C8 SPM 309 B 1 
HETATM 9 C C9 SPM . . . D 3 15.242 9.123 17.811 1 38.72 ? C9 SPM 309 B 1 
HETATM 10 N N10 SPM . . . D 3 16.297 9.928 18.398 1 40.22 ? N10 SPM 309 B 1 
HETATM 11 C C11 SPM . . . D 3 15.972 11.132 19.157 1 40.83 ? C11 SPM 309 B 1 
HETATM 12 C C12 SPM . . . D 3 17.218 11.864 19.646 1 42.17 ? C12 SPM 309 B 1 
HETATM 13 C C13 SPM . . . D 3 16.882 13.256 20.172 1 42.96 ? C13 SPM 309 B 1 
HETATM 14 N N14 SPM . . . D 3 16.718 13.207 21.613 1 44.49 ? N14 SPM 309 B 1 
#
_model_server_stats.io_time_ms              6 
_model_server_stats.parse_time_ms           10 
_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           14 
#