data_321D
#
_model_server_result.job_id            h62kxCABoLURVkagT1GENQ 
_model_server_result.datetime_utc      '2025-07-12 19:01:45' 
_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          321d 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":22}' 
#
_entry.id    321D 
#
_exptl.entry_id    321D 
_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            321D 
_cell.length_a            23.74 
_cell.length_b            40.89 
_cell.length_c            43.6 
_cell.Z_PDB               8 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 321D 
_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
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 DC 8 B DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog8 A N2 DG 3 A DG 3 1_555 B O2 DC 8 B DC 18 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog9 A O6 DG 3 A DG 3 1_555 B N4 DC 8 B DC 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 DC 8 A DC 8 1_555 B N1 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog23 A N4 DC 8 A DC 8 1_555 B O6 DG 3 B DG 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog24 A O2 DC 8 A DC 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 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                     321D 
_atom_sites.fract_transf_matrix[1][1]    0.042123 
_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]    0.024456 
_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]    0.022936 
_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 25 25 HOH HOH . 
E 3 HOH A 4 26 26 HOH HOH . 
E 3 HOH A 5 27 27 HOH HOH . 
E 3 HOH A 6 28 28 HOH HOH . 
E 3 HOH A 7 29 29 HOH HOH . 
E 3 HOH A 8 30 30 HOH HOH . 
E 3 HOH A 9 31 31 HOH HOH . 
E 3 HOH A 10 32 32 HOH HOH . 
E 3 HOH A 11 33 33 HOH HOH . 
E 3 HOH A 12 34 34 HOH HOH . 
E 3 HOH A 13 35 35 HOH HOH . 
E 3 HOH A 14 36 36 HOH HOH . 
E 3 HOH A 15 37 37 HOH HOH . 
E 3 HOH A 16 38 38 HOH HOH . 
E 3 HOH A 17 39 39 HOH HOH . 
E 3 HOH A 18 45 45 HOH HOH . 
E 3 HOH A 19 46 46 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 56 56 HOH HOH . 
E 3 HOH A 23 57 57 HOH HOH . 
E 3 HOH A 24 58 58 HOH HOH . 
E 3 HOH A 25 59 59 HOH HOH . 
E 3 HOH A 26 60 60 HOH HOH . 
E 3 HOH A 27 61 61 HOH HOH . 
E 3 HOH A 28 62 62 HOH HOH . 
E 3 HOH A 29 63 63 HOH HOH . 
E 3 HOH A 30 64 64 HOH HOH . 
E 3 HOH A 31 65 65 HOH HOH . 
E 3 HOH A 32 66 66 HOH HOH . 
E 3 HOH A 33 67 67 HOH HOH . 
E 3 HOH A 34 73 73 HOH HOH . 
E 3 HOH A 35 78 78 HOH HOH . 
E 3 HOH A 36 79 79 HOH HOH . 
E 3 HOH A 37 85 85 HOH HOH . 
E 3 HOH A 38 86 86 HOH HOH . 
E 3 HOH A 39 87 87 HOH HOH . 
E 3 HOH A 40 88 88 HOH HOH . 
E 3 HOH A 41 89 89 HOH HOH . 
E 3 HOH A 42 91 91 HOH HOH . 
E 3 HOH A 43 95 95 HOH HOH . 
E 3 HOH A 44 96 96 HOH HOH . 
E 3 HOH A 45 97 97 HOH HOH . 
E 3 HOH A 46 98 98 HOH HOH . 
E 3 HOH A 47 99 99 HOH HOH . 
E 3 HOH A 48 100 100 HOH HOH . 
E 3 HOH A 49 101 101 HOH HOH . 
E 3 HOH A 50 102 102 HOH HOH . 
E 3 HOH A 51 103 103 HOH HOH . 
E 3 HOH A 52 104 104 HOH HOH . 
E 3 HOH A 53 105 105 HOH HOH . 
E 3 HOH A 54 106 106 HOH HOH . 
E 3 HOH A 55 107 107 HOH HOH . 
E 3 HOH A 56 108 108 HOH HOH . 
F 3 HOH B 1 40 40 HOH HOH . 
F 3 HOH B 2 41 41 HOH HOH . 
F 3 HOH B 3 42 42 HOH HOH . 
F 3 HOH B 4 43 43 HOH HOH . 
F 3 HOH B 5 44 44 HOH HOH . 
F 3 HOH B 6 47 47 HOH HOH . 
F 3 HOH B 7 48 48 HOH HOH . 
F 3 HOH B 8 49 49 HOH HOH . 
F 3 HOH B 9 50 50 HOH HOH . 
F 3 HOH B 10 51 51 HOH HOH . 
F 3 HOH B 11 52 52 HOH HOH . 
F 3 HOH B 12 55 55 HOH HOH . 
F 3 HOH B 13 68 68 HOH HOH . 
F 3 HOH B 14 69 69 HOH HOH . 
F 3 HOH B 15 70 70 HOH HOH . 
F 3 HOH B 16 71 71 HOH HOH . 
F 3 HOH B 17 72 72 HOH HOH . 
F 3 HOH B 18 74 74 HOH HOH . 
F 3 HOH B 19 75 75 HOH HOH . 
F 3 HOH B 20 76 76 HOH HOH . 
F 3 HOH B 21 77 77 HOH HOH . 
F 3 HOH B 22 80 80 HOH HOH . 
F 3 HOH B 23 81 81 HOH HOH . 
F 3 HOH B 24 82 82 HOH HOH . 
F 3 HOH B 25 83 83 HOH HOH . 
F 3 HOH B 26 84 84 HOH HOH . 
F 3 HOH B 27 90 90 HOH HOH . 
F 3 HOH B 28 92 92 HOH HOH . 
F 3 HOH B 29 93 93 HOH HOH . 
F 3 HOH B 30 94 94 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 2 9.025 -17.646 0.799 1 42.84 ? N1 SPM 22 A 1 
HETATM 2 C C2 SPM . . . D 2 10.105 -17.203 1.656 1 37.87 ? C2 SPM 22 A 1 
HETATM 3 C C3 SPM . . . D 2 11.269 -16.752 0.796 1 38.42 ? C3 SPM 22 A 1 
HETATM 4 C C4 SPM . . . D 2 12.06 -15.73 1.551 1 35.22 ? C4 SPM 22 A 1 
HETATM 5 N N5 SPM . . . D 2 13.233 -15.287 0.832 1 33.28 ? N5 SPM 22 A 1 
HETATM 6 C C6 SPM . . . D 2 14.227 -15.048 1.852 1 29.32 ? C6 SPM 22 A 1 
HETATM 7 C C7 SPM . . . D 2 15.035 -13.832 1.49 1 32.88 ? C7 SPM 22 A 1 
HETATM 8 C C8 SPM . . . D 2 15.249 -13.046 2.76 1 36.9 ? C8 SPM 22 A 1 
HETATM 9 C C9 SPM . . . D 2 15.669 -11.64 2.401 1 38.26 ? C9 SPM 22 A 1 
HETATM 10 N N10 SPM . . . D 2 15.087 -10.694 3.335 1 38.99 ? N10 SPM 22 A 1 
HETATM 11 C C11 SPM . . . D 2 15.364 -9.355 2.859 1 37.63 ? C11 SPM 22 A 1 
HETATM 12 C C12 SPM . . . D 2 14.418 -8.366 3.528 1 38.31 ? C12 SPM 22 A 1 
HETATM 13 C C13 SPM . . . D 2 14.872 -6.939 3.274 1 37.82 ? C13 SPM 22 A 1 
HETATM 14 N N14 SPM . . . D 2 13.996 -5.996 3.946 1 39.43 ? N14 SPM 22 A 1 
#
_model_server_stats.io_time_ms              18 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    2 
_model_server_stats.query_time_ms           305 
_model_server_stats.encode_time_ms          2 
_model_server_stats.element_count           14 
#