data_1OFX
#
_model_server_result.job_id            6VaOgY13LFCl7WFyL5Sqkg 
_model_server_result.datetime_utc      '2024-10-18 14:35:29' 
_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          1ofx 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"C","auth_seq_id":21}' 
#
_entry.id    1OFX 
#
_exptl.entry_id    1OFX 
_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            1OFX 
_cell.length_a            24.03 
_cell.length_b            43.67 
_cell.length_c            48.95 
_cell.Z_PDB               4 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 1OFX 
_symmetry.cell_setting             orthorhombic 
_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 
_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                             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 N1 DG 1 A DG 1 1_555 B N3 DC 10 B DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog2 A N2 DG 1 A DG 1 1_555 B O2 DC 10 B DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog3 A O6 DG 1 A DG 1 1_555 B N4 DC 10 B DC 20 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog4 A N1 DG 2 A DG 2 1_555 B N3 DC 9 B DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog5 A N2 DG 2 A DG 2 1_555 B O2 DC 9 B DC 19 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog6 A O6 DG 2 A DG 2 1_555 B N4 DC 9 B DC 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 N3 DT 4 A DT 4 1_555 B N1 DA 7 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog11 A O4 DT 4 A DT 4 1_555 B N6 DA 7 B DA 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog12 A N1 DA 5 A DA 5 1_555 B N3 DT 6 B DT 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog13 A N6 DA 5 A DA 5 1_555 B O4 DT 6 B DT 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog14 A N3 DT 6 A DT 6 1_555 B N1 DA 5 B DA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog15 A O4 DT 6 A DT 6 1_555 B N6 DA 5 B DA 15 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog16 A N1 DA 7 A DA 7 1_555 B N3 DT 4 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog17 A N6 DA 7 A DA 7 1_555 B O4 DT 4 B DT 14 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog18 A N3 DC 8 A DC 8 1_555 B N1 G 3 B G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog19 A N4 DC 8 A DC 8 1_555 B O6 G 3 B G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog20 A O2 DC 8 A DC 8 1_555 B N2 G 3 B G 13 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog21 A N1 DG 9 A DG 9 1_555 B N3 C 2 B C 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog22 A N2 DG 9 A DG 9 1_555 B O2 C 2 B C 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog23 A O6 DG 9 A DG 9 1_555 B N4 C 2 B C 12 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog24 A N3 DC 10 A DC 10 1_555 B N1 G 1 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog25 A N4 DC 10 A DC 10 1_555 B O6 G 1 B G 11 1_555 ? ? ? ? ? ? ? ? ? ? ? ? ? ? 
hydrog WATSON-CRICK hydrog26 A O2 DC 10 A DC 10 1_555 B N2 G 1 B G 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 228 n n 
N1 HN11 SPM sing 229 n n 
N1 HN12 SPM sing 230 n n 
C2 C3 SPM sing 231 n n 
C2 H21 SPM sing 232 n n 
C2 H22 SPM sing 233 n n 
C3 C4 SPM sing 234 n n 
C3 H31 SPM sing 235 n n 
C3 H32 SPM sing 236 n n 
C4 N5 SPM sing 237 n n 
C4 H41 SPM sing 238 n n 
C4 H42 SPM sing 239 n n 
N5 C6 SPM sing 240 n n 
N5 HN5 SPM sing 241 n n 
C6 C7 SPM sing 242 n n 
C6 H61 SPM sing 243 n n 
C6 H62 SPM sing 244 n n 
C7 C8 SPM sing 245 n n 
C7 H71 SPM sing 246 n n 
C7 H72 SPM sing 247 n n 
C8 C9 SPM sing 248 n n 
C8 H81 SPM sing 249 n n 
C8 H82 SPM sing 250 n n 
C9 N10 SPM sing 251 n n 
C9 H91 SPM sing 252 n n 
C9 H92 SPM sing 253 n n 
N10 C11 SPM sing 254 n n 
N10 HN0 SPM sing 255 n n 
C11 C12 SPM sing 256 n n 
C11 H111 SPM sing 257 n n 
C11 H112 SPM sing 258 n n 
C12 C13 SPM sing 259 n n 
C12 H121 SPM sing 260 n n 
C12 H122 SPM sing 261 n n 
C13 N14 SPM sing 262 n n 
C13 H131 SPM sing 263 n n 
C13 H132 SPM sing 264 n n 
N14 HN41 SPM sing 265 n n 
N14 HN42 SPM sing 266 n n 
#
_atom_sites.entry_id                     1OFX 
_atom_sites.fract_transf_matrix[1][1]    0.041615 
_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]    0.022899 
_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]    0.020429 
_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 3 SPM B 1 21 21 SPM SPM . 
D 4 HOH A 1 23 23 HOH HOH . 
D 4 HOH A 2 27 27 HOH HOH . 
D 4 HOH A 3 28 28 HOH HOH . 
D 4 HOH A 4 29 29 HOH HOH . 
D 4 HOH A 5 31 31 HOH HOH . 
D 4 HOH A 6 33 33 HOH HOH . 
D 4 HOH A 7 34 34 HOH HOH . 
D 4 HOH A 8 39 39 HOH HOH . 
D 4 HOH A 9 40 40 HOH HOH . 
D 4 HOH A 10 47 47 HOH HOH . 
D 4 HOH A 11 50 50 HOH HOH . 
D 4 HOH A 12 52 52 HOH HOH . 
D 4 HOH A 13 53 53 HOH HOH . 
D 4 HOH A 14 56 56 HOH HOH . 
D 4 HOH A 15 57 57 HOH HOH . 
D 4 HOH A 16 61 61 HOH HOH . 
D 4 HOH A 17 69 69 HOH HOH . 
D 4 HOH A 18 72 72 HOH HOH . 
D 4 HOH A 19 74 74 HOH HOH . 
D 4 HOH A 20 78 78 HOH HOH . 
D 4 HOH A 21 79 79 HOH HOH . 
D 4 HOH A 22 80 80 HOH HOH . 
D 4 HOH A 23 81 81 HOH HOH . 
D 4 HOH A 24 83 83 HOH HOH . 
D 4 HOH A 25 84 84 HOH HOH . 
D 4 HOH A 26 92 92 HOH HOH . 
D 4 HOH A 27 93 93 HOH HOH . 
D 4 HOH A 28 97 97 HOH HOH . 
D 4 HOH A 29 98 98 HOH HOH . 
D 4 HOH A 30 101 101 HOH HOH . 
D 4 HOH A 31 111 111 HOH HOH . 
E 4 HOH B 1 22 22 HOH HOH . 
E 4 HOH B 2 24 24 HOH HOH . 
E 4 HOH B 3 25 25 HOH HOH . 
E 4 HOH B 4 26 26 HOH HOH . 
E 4 HOH B 5 30 30 HOH HOH . 
E 4 HOH B 6 32 32 HOH HOH . 
E 4 HOH B 7 35 35 HOH HOH . 
E 4 HOH B 8 36 36 HOH HOH . 
E 4 HOH B 9 37 37 HOH HOH . 
E 4 HOH B 10 38 38 HOH HOH . 
E 4 HOH B 11 41 41 HOH HOH . 
E 4 HOH B 12 42 42 HOH HOH . 
E 4 HOH B 13 43 43 HOH HOH . 
E 4 HOH B 14 44 44 HOH HOH . 
E 4 HOH B 15 45 45 HOH HOH . 
E 4 HOH B 16 46 46 HOH HOH . 
E 4 HOH B 17 48 48 HOH HOH . 
E 4 HOH B 18 49 49 HOH HOH . 
E 4 HOH B 19 51 51 HOH HOH . 
E 4 HOH B 20 54 54 HOH HOH . 
E 4 HOH B 21 55 55 HOH HOH . 
E 4 HOH B 22 58 58 HOH HOH . 
E 4 HOH B 23 59 59 HOH HOH . 
E 4 HOH B 24 60 60 HOH HOH . 
E 4 HOH B 25 62 62 HOH HOH . 
E 4 HOH B 26 63 63 HOH HOH . 
E 4 HOH B 27 64 64 HOH HOH . 
E 4 HOH B 28 65 65 HOH HOH . 
E 4 HOH B 29 66 66 HOH HOH . 
E 4 HOH B 30 67 67 HOH HOH . 
E 4 HOH B 31 68 68 HOH HOH . 
E 4 HOH B 32 70 70 HOH HOH . 
E 4 HOH B 33 71 71 HOH HOH . 
E 4 HOH B 34 73 73 HOH HOH . 
E 4 HOH B 35 75 75 HOH HOH . 
E 4 HOH B 36 76 76 HOH HOH . 
E 4 HOH B 37 77 77 HOH HOH . 
E 4 HOH B 38 82 82 HOH HOH . 
E 4 HOH B 39 85 85 HOH HOH . 
E 4 HOH B 40 86 86 HOH HOH . 
E 4 HOH B 41 87 87 HOH HOH . 
E 4 HOH B 42 88 88 HOH HOH . 
E 4 HOH B 43 89 89 HOH HOH . 
E 4 HOH B 44 90 90 HOH HOH . 
E 4 HOH B 45 91 91 HOH HOH . 
E 4 HOH B 46 94 94 HOH HOH . 
E 4 HOH B 47 95 95 HOH HOH . 
E 4 HOH B 48 96 96 HOH HOH . 
E 4 HOH B 49 99 99 HOH HOH . 
E 4 HOH B 50 100 100 HOH HOH . 
E 4 HOH B 51 102 102 HOH HOH . 
E 4 HOH B 52 103 103 HOH HOH . 
E 4 HOH B 53 104 104 HOH HOH . 
E 4 HOH B 54 105 105 HOH HOH . 
E 4 HOH B 55 106 106 HOH HOH . 
E 4 HOH B 56 107 107 HOH HOH . 
E 4 HOH B 57 108 108 HOH HOH . 
E 4 HOH B 58 109 109 HOH HOH . 
E 4 HOH B 59 110 110 HOH HOH . 
E 4 HOH B 60 112 112 HOH HOH . 
E 4 HOH B 61 113 113 HOH HOH . 
E 4 HOH B 62 114 114 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 5.647 9.401 28.377 1 30.67 ? N1 SPM 21 B 1 
HETATM 2 C C2 SPM . . . C 3 6.925 9.908 27.67 1 30.61 ? C2 SPM 21 B 1 
HETATM 3 C C3 SPM . . . C 3 6.651 11.152 26.802 1 30.57 ? C3 SPM 21 B 1 
HETATM 4 C C4 SPM . . . C 3 7.162 12.43 27.526 1 30.65 ? C4 SPM 21 B 1 
HETATM 5 N N5 SPM . . . C 3 6.769 12.397 29.035 1 30.36 ? N5 SPM 21 B 1 
HETATM 6 C C6 SPM . . . C 3 7.432 13.476 29.892 1 29.67 ? C6 SPM 21 B 1 
HETATM 7 C C7 SPM . . . C 3 8.818 13.102 30.41 1 29.14 ? C7 SPM 21 B 1 
HETATM 8 C C8 SPM . . . C 3 9.968 13.711 29.63 1 28.74 ? C8 SPM 21 B 1 
HETATM 9 C C9 SPM . . . C 3 9.608 14.281 28.254 1 28.34 ? C9 SPM 21 B 1 
HETATM 10 N N10 SPM . . . C 3 9.675 15.815 28.251 1 28.35 ? N10 SPM 21 B 1 
HETATM 11 C C11 SPM . . . C 3 8.793 16.463 27.169 1 28.32 ? C11 SPM 21 B 1 
HETATM 12 C C12 SPM . . . C 3 9.514 17.623 26.483 1 28.16 ? C12 SPM 21 B 1 
HETATM 13 C C13 SPM . . . C 3 8.848 18.991 26.729 1 28.3 ? C13 SPM 21 B 1 
HETATM 14 N N14 SPM . . . C 3 9.835 20.111 26.275 1 28.33 ? N14 SPM 21 B 1 
#
_model_server_stats.io_time_ms              10 
_model_server_stats.parse_time_ms           6 
_model_server_stats.create_model_time_ms    1 
_model_server_stats.query_time_ms           243 
_model_server_stats.encode_time_ms          5 
_model_server_stats.element_count           14 
#