data_1D12
#
_model_server_result.job_id            FgUxqyjmvfFnW7tbPIFdPg 
_model_server_result.datetime_utc      '2025-03-06 00:11:07' 
_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          1d12 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":8}' 
#
_entry.id    1D12 
#
_exptl.entry_id    1D12 
_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         90 
_cell.entry_id            1D12 
_cell.length_a            28.21 
_cell.length_b            28.21 
_cell.length_c            53.19 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1D12 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        92 
_symmetry.space_group_name_Hall    . 
_symmetry.space_group_name_H-M     'P 41 21 2' 
#
_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 
_pdbx_struct_assembly_gen.assembly_id        1 
_pdbx_struct_assembly_gen.oper_expression    1,2 
#
loop_
_pdbx_struct_oper_list.id
_pdbx_struct_oper_list.type
_pdbx_struct_oper_list.name
_pdbx_struct_oper_list.symmetry_operation
_pdbx_struct_oper_list.matrix[1][1]
_pdbx_struct_oper_list.matrix[1][2]
_pdbx_struct_oper_list.matrix[1][3]
_pdbx_struct_oper_list.matrix[2][1]
_pdbx_struct_oper_list.matrix[2][2]
_pdbx_struct_oper_list.matrix[2][3]
_pdbx_struct_oper_list.matrix[3][1]
_pdbx_struct_oper_list.matrix[3][2]
_pdbx_struct_oper_list.matrix[3][3]
_pdbx_struct_oper_list.vector[1]
_pdbx_struct_oper_list.vector[2]
_pdbx_struct_oper_list.vector[3]
1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 
2 'crystal symmetry operation' 8_665 -y+1,-x+1,-z+1/2 0 -1 0 -1 0 0 0 0 -1 28.21 28.21 26.595 
#
_struct_asym.details                        ? 
_struct_asym.entity_id                      3 
_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
metalc ? metalc1 A N7 DG 6 A DG 6 1_555 D NA NA . A NA 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.781 ? 
metalc ? metalc2 D NA NA . A NA 9 1_555 E O HOH . A HOH 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.822 ? 
hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 A N1 DG 6 A DG 6 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 A O6 DG 6 A DG 6 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 A N2 DG 6 A DG 6 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 A N3 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 A O2 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 A N4 DC 5 A DC 5 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N1 DA 3 A DA 3 1_555 A N3 DT 4 A DT 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N6 DA 3 A DA 3 1_555 A O4 DT 4 A DT 4 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A N3 DT 4 A DT 4 1_555 A N1 DA 3 A DA 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A O4 DT 4 A DT 4 1_555 A N6 DA 3 A DA 3 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N3 DC 5 A DC 5 1_555 A N1 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A N4 DC 5 A DC 5 1_555 A O6 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A O2 DC 5 A DC 5 1_555 A N2 DG 2 A DG 2 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N1 DG 6 A DG 6 1_555 A N3 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A N2 DG 6 A DG 6 1_555 A O2 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A O6 DG 6 A DG 6 1_555 A N4 DC 1 A DC 1 8_665 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
#
_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 224 n n 
N1 HN11 SPM sing 225 n n 
N1 HN12 SPM sing 226 n n 
C2 C3 SPM sing 227 n n 
C2 H21 SPM sing 228 n n 
C2 H22 SPM sing 229 n n 
C3 C4 SPM sing 230 n n 
C3 H31 SPM sing 231 n n 
C3 H32 SPM sing 232 n n 
C4 N5 SPM sing 233 n n 
C4 H41 SPM sing 234 n n 
C4 H42 SPM sing 235 n n 
N5 C6 SPM sing 236 n n 
N5 HN5 SPM sing 237 n n 
C6 C7 SPM sing 238 n n 
C6 H61 SPM sing 239 n n 
C6 H62 SPM sing 240 n n 
C7 C8 SPM sing 241 n n 
C7 H71 SPM sing 242 n n 
C7 H72 SPM sing 243 n n 
C8 C9 SPM sing 244 n n 
C8 H81 SPM sing 245 n n 
C8 H82 SPM sing 246 n n 
C9 N10 SPM sing 247 n n 
C9 H91 SPM sing 248 n n 
C9 H92 SPM sing 249 n n 
N10 C11 SPM sing 250 n n 
N10 HN0 SPM sing 251 n n 
C11 C12 SPM sing 252 n n 
C11 H111 SPM sing 253 n n 
C11 H112 SPM sing 254 n n 
C12 C13 SPM sing 255 n n 
C12 H121 SPM sing 256 n n 
C12 H122 SPM sing 257 n n 
C13 N14 SPM sing 258 n n 
C13 H131 SPM sing 259 n n 
C13 H132 SPM sing 260 n n 
N14 HN41 SPM sing 261 n n 
N14 HN42 SPM sing 262 n n 
#
_atom_sites.entry_id                     1D12 
_atom_sites.fract_transf_matrix[1][1]    0.035448 
_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]    0.035448 
_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]    0.018801 
_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 DM2 A 1 7 7 DM2 DM2 . 
C 3 SPM A 1 8 8 SPM SPM . 
D 4 NA A 1 9 9 NA NA . 
E 5 HOH A 1 10 10 HOH HOH . 
E 5 HOH A 2 11 11 HOH HOH . 
E 5 HOH A 3 12 12 HOH HOH . 
E 5 HOH A 4 13 13 HOH HOH . 
E 5 HOH A 5 14 14 HOH HOH . 
E 5 HOH A 6 15 15 HOH HOH . 
E 5 HOH A 7 16 16 HOH HOH . 
E 5 HOH A 8 17 17 HOH HOH . 
E 5 HOH A 9 18 18 HOH HOH . 
E 5 HOH A 10 19 19 HOH HOH . 
E 5 HOH A 11 20 20 HOH HOH . 
E 5 HOH A 12 21 21 HOH HOH . 
E 5 HOH A 13 22 22 HOH HOH . 
E 5 HOH A 14 23 23 HOH HOH . 
E 5 HOH A 15 24 24 HOH HOH . 
E 5 HOH A 16 25 25 HOH HOH . 
E 5 HOH A 17 26 26 HOH HOH . 
E 5 HOH A 18 27 27 HOH HOH . 
E 5 HOH A 19 28 28 HOH HOH . 
E 5 HOH A 20 29 29 HOH HOH . 
E 5 HOH A 21 30 30 HOH HOH . 
E 5 HOH A 22 31 31 HOH HOH . 
E 5 HOH A 23 32 32 HOH HOH . 
E 5 HOH A 24 33 33 HOH HOH . 
E 5 HOH A 25 34 34 HOH HOH . 
E 5 HOH A 26 35 35 HOH HOH . 
E 5 HOH A 27 36 36 HOH HOH . 
E 5 HOH A 28 37 37 HOH HOH . 
E 5 HOH A 29 38 38 HOH HOH . 
E 5 HOH A 30 39 39 HOH HOH . 
E 5 HOH A 31 40 40 HOH HOH . 
E 5 HOH A 32 41 41 HOH HOH . 
E 5 HOH A 33 42 42 HOH HOH . 
E 5 HOH A 34 43 43 HOH HOH . 
E 5 HOH A 35 44 44 HOH HOH . 
E 5 HOH A 36 45 45 HOH HOH . 
E 5 HOH A 37 46 46 HOH HOH . 
E 5 HOH A 38 47 47 HOH HOH . 
E 5 HOH A 39 48 48 HOH HOH . 
E 5 HOH A 40 49 49 HOH HOH . 
E 5 HOH A 41 50 50 HOH HOH . 
E 5 HOH A 42 51 51 HOH HOH . 
E 5 HOH A 43 52 52 HOH HOH . 
E 5 HOH A 44 53 53 HOH HOH . 
E 5 HOH A 45 54 54 HOH HOH . 
E 5 HOH A 46 55 55 HOH HOH . 
E 5 HOH A 47 56 56 HOH HOH . 
E 5 HOH A 48 57 57 HOH HOH . 
E 5 HOH A 49 58 58 HOH HOH . 
E 5 HOH A 50 59 59 HOH HOH . 
E 5 HOH A 51 60 60 HOH HOH . 
E 5 HOH A 52 61 61 HOH HOH . 
E 5 HOH A 53 62 62 HOH HOH . 
E 5 HOH A 54 63 63 HOH HOH . 
E 5 HOH A 55 64 64 HOH HOH . 
E 5 HOH A 56 65 65 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 3 19.825 19.281 8.507 1 40.45 ? N1 SPM 8 A 1 
HETATM 2 C C2 SPM . . . C 3 18.593 20.028 7.938 1 40.21 ? C2 SPM 8 A 1 
HETATM 3 C C3 SPM . . . C 3 17.768 20.519 9.122 1 40.41 ? C3 SPM 8 A 1 
HETATM 4 C C4 SPM . . . C 3 16.333 21.019 8.723 1 40.24 ? C4 SPM 8 A 1 
HETATM 5 N N5 SPM . . . C 3 15.696 21.164 10.198 1 40.49 ? N5 SPM 8 A 1 
HETATM 6 C C6 SPM . . . C 3 14.211 21.542 10.016 1 40.34 ? C6 SPM 8 A 1 
HETATM 7 C C7 SPM . . . C 3 13.458 21.001 11.246 1 40.17 ? C7 SPM 8 A 1 
HETATM 8 C C8 SPM . . . C 3 13.798 19.477 11.413 1 39.83 ? C8 SPM 8 A 1 
HETATM 9 C C9 SPM . . . C 3 12.569 18.814 12.044 1 39.94 ? C9 SPM 8 A 1 
HETATM 10 N N10 SPM . . . C 3 11.454 18.521 11.044 1 40.07 ? N10 SPM 8 A 1 
HETATM 11 C C11 SPM . . . C 3 10.684 19.764 10.468 1 40.04 ? C11 SPM 8 A 1 
HETATM 12 C C12 SPM . . . C 3 10.409 19.504 8.978 1 40.13 ? C12 SPM 8 A 1 
HETATM 13 C C13 SPM . . . C 3 8.947 19.684 8.566 1 40.34 ? C13 SPM 8 A 1 
HETATM 14 N N14 SPM . . . C 3 8.929 20.208 7.076 1 40.38 ? N14 SPM 8 A 1 
#
_model_server_stats.io_time_ms              5 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           264 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           14 
#