data_324D
#
_model_server_result.job_id            GWvyjK-Kgs74WsEcWUduXA 
_model_server_result.datetime_utc      '2025-07-12 19:03:08' 
_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          324d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":21}' 
#
_entry.id    324D 
#
_exptl.entry_id    324D 
_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            324D 
_cell.length_a            23.64 
_cell.length_b            40.82 
_cell.length_c            43.44 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 324D 
_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 
_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 D 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
covale ? covale1 A O3' DC 7 A DC 7 1_555 A P 5CM 8 A 5CM 8 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.615 ? 
covale ? covale2 A O3' 5CM 8 A 5CM 8 1_555 A P DG 9 A DG 9 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.593 ? 
covale ? covale3 B O3' DC 7 B DC 17 1_555 B P 5CM 8 B 5CM 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.61 ? 
covale ? covale4 B O3' 5CM 8 B 5CM 18 1_555 B P DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.622 ? 
hydrog WATSON-CRICK hydrog1 A N3 DC 1 A DC 1 1_555 B N1 DG 10 B DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N4 DC 1 A DC 1 1_555 B O6 DG 10 B DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O2 DC 1 A DC 1 1_555 B N2 DG 10 B DG 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N3 DC 2 A DC 2 1_555 B N1 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N4 DC 2 A DC 2 1_555 B O6 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O2 DC 2 A DC 2 1_555 B N2 DG 9 B DG 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog7 A N1 DG 3 A DG 3 1_555 B N3 5CM 8 B 5CM 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N2 DG 3 A DG 3 1_555 B O2 5CM 8 B 5CM 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A O6 DG 3 A DG 3 1_555 B N4 5CM 8 B 5CM 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog10 A N1 DG 4 A DG 4 1_555 B N3 DC 7 B DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A N2 DG 4 A DG 4 1_555 B O2 DC 7 B DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A O6 DG 4 A DG 4 1_555 B N4 DC 7 B DC 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A N1 DG 5 A DG 5 1_555 B N3 DC 6 B DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N2 DG 5 A DG 5 1_555 B O2 DC 6 B DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A O6 DG 5 A DG 5 1_555 B N4 DC 6 B DC 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A N3 DC 6 A DC 6 1_555 B N1 DG 5 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A N4 DC 6 A DC 6 1_555 B O6 DG 5 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A O2 DC 6 A DC 6 1_555 B N2 DG 5 B DG 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog19 A N3 DC 7 A DC 7 1_555 B N1 DG 4 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog20 A N4 DC 7 A DC 7 1_555 B O6 DG 4 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog21 A O2 DC 7 A DC 7 1_555 B N2 DG 4 B DG 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog22 A N3 5CM 8 A 5CM 8 1_555 B N1 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog23 A N4 5CM 8 A 5CM 8 1_555 B O6 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog24 A O2 5CM 8 A 5CM 8 1_555 B N2 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog25 A N1 DG 9 A DG 9 1_555 B N3 DC 2 B DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog26 A N2 DG 9 A DG 9 1_555 B O2 DC 2 B DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog27 A O6 DG 9 A DG 9 1_555 B N4 DC 2 B DC 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog28 A N1 DG 10 A DG 10 1_555 B N3 DC 1 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog29 A N2 DG 10 A DG 10 1_555 B O2 DC 1 B DC 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog30 A O6 DG 10 A DG 10 1_555 B N4 DC 1 B DC 11 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 115 n n 
N1 HN11 SPM sing 116 n n 
N1 HN12 SPM sing 117 n n 
C2 C3 SPM sing 118 n n 
C2 H21 SPM sing 119 n n 
C2 H22 SPM sing 120 n n 
C3 C4 SPM sing 121 n n 
C3 H31 SPM sing 122 n n 
C3 H32 SPM sing 123 n n 
C4 N5 SPM sing 124 n n 
C4 H41 SPM sing 125 n n 
C4 H42 SPM sing 126 n n 
N5 C6 SPM sing 127 n n 
N5 HN5 SPM sing 128 n n 
C6 C7 SPM sing 129 n n 
C6 H61 SPM sing 130 n n 
C6 H62 SPM sing 131 n n 
C7 C8 SPM sing 132 n n 
C7 H71 SPM sing 133 n n 
C7 H72 SPM sing 134 n n 
C8 C9 SPM sing 135 n n 
C8 H81 SPM sing 136 n n 
C8 H82 SPM sing 137 n n 
C9 N10 SPM sing 138 n n 
C9 H91 SPM sing 139 n n 
C9 H92 SPM sing 140 n n 
N10 C11 SPM sing 141 n n 
N10 HN0 SPM sing 142 n n 
C11 C12 SPM sing 143 n n 
C11 H111 SPM sing 144 n n 
C11 H112 SPM sing 145 n n 
C12 C13 SPM sing 146 n n 
C12 H121 SPM sing 147 n n 
C12 H122 SPM sing 148 n n 
C13 N14 SPM sing 149 n n 
C13 H131 SPM sing 150 n n 
C13 H132 SPM sing 151 n n 
N14 HN41 SPM sing 152 n n 
N14 HN42 SPM sing 153 n n 
#
_atom_sites.entry_id                     324D 
_atom_sites.fract_transf_matrix[1][1]    0.042301 
_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]    0.024498 
_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]    0.02302 
_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 21 21 SPM SPM . 
D 2 SPM A 1 22 22 SPM SPM . 
E 3 HOH A 1 23 23 HOH HOH . 
E 3 HOH A 2 24 24 HOH HOH . 
E 3 HOH A 3 27 27 HOH HOH . 
E 3 HOH A 4 30 30 HOH HOH . 
E 3 HOH A 5 32 32 HOH HOH . 
E 3 HOH A 6 33 33 HOH HOH . 
E 3 HOH A 7 34 34 HOH HOH . 
E 3 HOH A 8 35 35 HOH HOH . 
E 3 HOH A 9 36 36 HOH HOH . 
E 3 HOH A 10 37 37 HOH HOH . 
E 3 HOH A 11 38 38 HOH HOH . 
E 3 HOH A 12 40 40 HOH HOH . 
E 3 HOH A 13 41 41 HOH HOH . 
E 3 HOH A 14 44 44 HOH HOH . 
E 3 HOH A 15 45 45 HOH HOH . 
E 3 HOH A 16 47 47 HOH HOH . 
E 3 HOH A 17 49 49 HOH HOH . 
E 3 HOH A 18 50 50 HOH HOH . 
E 3 HOH A 19 51 51 HOH HOH . 
E 3 HOH A 20 53 53 HOH HOH . 
E 3 HOH A 21 54 54 HOH HOH . 
E 3 HOH A 22 55 55 HOH HOH . 
E 3 HOH A 23 56 56 HOH HOH . 
E 3 HOH A 24 59 59 HOH HOH . 
E 3 HOH A 25 67 67 HOH HOH . 
E 3 HOH A 26 68 68 HOH HOH . 
E 3 HOH A 27 69 69 HOH HOH . 
E 3 HOH A 28 70 70 HOH HOH . 
E 3 HOH A 29 71 71 HOH HOH . 
E 3 HOH A 30 75 75 HOH HOH . 
E 3 HOH A 31 76 76 HOH HOH . 
E 3 HOH A 32 83 83 HOH HOH . 
E 3 HOH A 33 84 84 HOH HOH . 
E 3 HOH A 34 85 85 HOH HOH . 
F 3 HOH B 1 25 25 HOH HOH . 
F 3 HOH B 2 26 26 HOH HOH . 
F 3 HOH B 3 28 28 HOH HOH . 
F 3 HOH B 4 29 29 HOH HOH . 
F 3 HOH B 5 31 31 HOH HOH . 
F 3 HOH B 6 39 39 HOH HOH . 
F 3 HOH B 7 42 42 HOH HOH . 
F 3 HOH B 8 43 43 HOH HOH . 
F 3 HOH B 9 46 46 HOH HOH . 
F 3 HOH B 10 48 48 HOH HOH . 
F 3 HOH B 11 52 52 HOH HOH . 
F 3 HOH B 12 57 57 HOH HOH . 
F 3 HOH B 13 58 58 HOH HOH . 
F 3 HOH B 14 60 60 HOH HOH . 
F 3 HOH B 15 61 61 HOH HOH . 
F 3 HOH B 16 62 62 HOH HOH . 
F 3 HOH B 17 63 63 HOH HOH . 
F 3 HOH B 18 64 64 HOH HOH . 
F 3 HOH B 19 65 65 HOH HOH . 
F 3 HOH B 20 66 66 HOH HOH . 
F 3 HOH B 21 72 72 HOH HOH . 
F 3 HOH B 22 73 73 HOH HOH . 
F 3 HOH B 23 74 74 HOH HOH . 
F 3 HOH B 24 77 77 HOH HOH . 
F 3 HOH B 25 78 78 HOH HOH . 
F 3 HOH B 26 79 79 HOH HOH . 
F 3 HOH B 27 80 80 HOH HOH . 
F 3 HOH B 28 81 81 HOH HOH . 
F 3 HOH B 29 82 82 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 9.522 9.114 14.448 1 39.55 ? N1 SPM 21 A 1 
HETATM 2 C C2 SPM . . . C 2 8.814 8.023 13.812 1 33.89 ? C2 SPM 21 A 1 
HETATM 3 C C3 SPM . . . C 2 8.558 8.425 12.373 1 29.74 ? C3 SPM 21 A 1 
HETATM 4 C C4 SPM . . . C 2 7.735 7.419 11.592 1 32.57 ? C4 SPM 21 A 1 
HETATM 5 N N5 SPM . . . C 2 7.335 8.055 10.352 1 32.69 ? N5 SPM 21 A 1 
HETATM 6 C C6 SPM . . . C 2 7.321 7.105 9.257 1 34.49 ? C6 SPM 21 A 1 
HETATM 7 C C7 SPM . . . C 2 6.863 7.798 7.986 1 37.85 ? C7 SPM 21 A 1 
HETATM 8 C C8 SPM . . . C 2 6.848 6.883 6.783 1 13.84 ? C8 SPM 21 A 1 
HETATM 9 C C9 SPM . . . C 2 5.897 7.581 5.842 1 22.28 ? C9 SPM 21 A 1 
HETATM 10 N N10 SPM . . . C 2 5.362 6.591 4.956 1 22.67 ? N10 SPM 21 A 1 
HETATM 11 C C11 SPM . . . C 2 3.932 6.653 5.135 1 25.91 ? C11 SPM 21 A 1 
HETATM 12 C C12 SPM . . . C 2 3.398 5.266 4.872 1 18.55 ? C12 SPM 21 A 1 
HETATM 13 C C13 SPM . . . C 2 2.622 4.756 6.07 1 25.34 ? C13 SPM 21 A 1 
HETATM 14 N N14 SPM . . . C 2 2.273 3.349 5.969 1 34.54 ? N14 SPM 21 A 1 
#
_model_server_stats.io_time_ms              11 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           279 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           14 
#