data_7N78
#
_model_server_result.job_id            za6F7BJY0JHPy3c_wXyZrw 
_model_server_result.datetime_utc      '2024-11-21 13:49:02' 
_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          7n78 
#
_model_server_params.name     atom_site 
_model_server_params.value    '{"label_asym_id":"D","auth_seq_id":1203}' 
#
_entry.id    7N78 
#
_exptl.entry_id    7N78 
_exptl.method      'ELECTRON MICROSCOPY' 
#
_entity.details                     ? 
_entity.formula_weight              202.34 
_entity.id                          4 
_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            7N78 
_cell.length_a            1 
_cell.length_b            1 
_cell.length_c            1 
_cell.Z_PDB               ? 
_cell.pdbx_unique_axis    ? 
#
_symmetry.entry_id                 7N78 
_symmetry.cell_setting             ? 
_symmetry.Int_Tables_number        1 
_symmetry.space_group_name_Hall    ? 
_symmetry.space_group_name_H-M     'P 1' 
#
_pdbx_struct_assembly.method_details        ? 
_pdbx_struct_assembly.oligomeric_details    monomeric 
_pdbx_struct_assembly.oligomeric_count      1 
_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,G,H,I,J,K,L,M 
_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    ? 
_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                      4 
_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
metalc ? metalc1 A OD2 ASP 508 A ASP 508 1_555 C MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.93 ? 
metalc ? metalc2 A O THR 510 A THR 510 1_555 C MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.245 ? 
metalc ? metalc3 A OD1 ASP 873 A ASP 873 1_555 C MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.672 ? 
metalc ? metalc4 B O2 PO4 . A PO4 1201 1_555 C MG MG . A MG 1202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.95 ? 
#
_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 517 n n 
N1 HN11 SPM sing 518 n n 
N1 HN12 SPM sing 519 n n 
C2 C3 SPM sing 520 n n 
C2 H21 SPM sing 521 n n 
C2 H22 SPM sing 522 n n 
C3 C4 SPM sing 523 n n 
C3 H31 SPM sing 524 n n 
C3 H32 SPM sing 525 n n 
C4 N5 SPM sing 526 n n 
C4 H41 SPM sing 527 n n 
C4 H42 SPM sing 528 n n 
N5 C6 SPM sing 529 n n 
N5 HN5 SPM sing 530 n n 
C6 C7 SPM sing 531 n n 
C6 H61 SPM sing 532 n n 
C6 H62 SPM sing 533 n n 
C7 C8 SPM sing 534 n n 
C7 H71 SPM sing 535 n n 
C7 H72 SPM sing 536 n n 
C8 C9 SPM sing 537 n n 
C8 H81 SPM sing 538 n n 
C8 H82 SPM sing 539 n n 
C9 N10 SPM sing 540 n n 
C9 H91 SPM sing 541 n n 
C9 H92 SPM sing 542 n n 
N10 C11 SPM sing 543 n n 
N10 HN0 SPM sing 544 n n 
C11 C12 SPM sing 545 n n 
C11 H111 SPM sing 546 n n 
C11 H112 SPM sing 547 n n 
C12 C13 SPM sing 548 n n 
C12 H121 SPM sing 549 n n 
C12 H122 SPM sing 550 n n 
C13 N14 SPM sing 551 n n 
C13 H131 SPM sing 552 n n 
C13 H132 SPM sing 553 n n 
N14 HN41 SPM sing 554 n n 
N14 HN42 SPM sing 555 n n 
#
_atom_sites.entry_id                     7N78 
_atom_sites.fract_transf_matrix[1][1]    1 
_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]    1 
_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]    1 
_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 PO4 A 1 1201 1201 PO4 PO4 . 
C 3 MG A 1 1202 1202 MG MG . 
D 4 SPM A 1 1203 1301 SPM SPM . 
E 5 Y01 A 1 1204 1401 Y01 Y01 . 
F 5 Y01 A 1 1205 1402 Y01 Y01 . 
G 6 PC1 A 1 1206 1403 PC1 PC1 . 
H 7 LMT A 1 1207 1404 LMT LMT . 
I 7 LMT A 1 1208 1405 LMT LMT . 
J 7 LMT A 1 1209 1406 LMT LMT . 
K 6 PC1 A 1 1210 1407 PC1 PC1 . 
L 5 Y01 A 1 1211 1408 Y01 Y01 . 
M 8 HOH A 1 1301 1306 HOH HOH . 
M 8 HOH A 2 1302 1303 HOH HOH . 
M 8 HOH A 3 1303 1302 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 4 138.421 152.493 130.662 1 44.09 ? N1 SPM 1203 A 1 
HETATM 2 C C2 SPM . . . D 4 138.869 153.523 129.721 1 44.09 ? C2 SPM 1203 A 1 
HETATM 3 C C3 SPM . . . D 4 137.892 154.689 129.738 1 44.09 ? C3 SPM 1203 A 1 
HETATM 4 C C4 SPM . . . D 4 137.159 154.723 128.404 1 44.09 ? C4 SPM 1203 A 1 
HETATM 5 N N5 SPM . . . D 4 136.179 155.812 128.396 1 44.09 ? N5 SPM 1203 A 1 
HETATM 6 C C6 SPM . . . D 4 135.422 155.639 127.156 1 44.09 ? C6 SPM 1203 A 1 
HETATM 7 C C7 SPM . . . D 4 134.434 156.783 126.956 1 44.09 ? C7 SPM 1203 A 1 
HETATM 8 C C8 SPM . . . D 4 133.841 156.662 125.555 1 44.09 ? C8 SPM 1203 A 1 
HETATM 9 C C9 SPM . . . D 4 132.934 157.853 125.265 1 44.09 ? C9 SPM 1203 A 1 
HETATM 10 N N10 SPM . . . D 4 132.524 157.821 123.855 1 44.09 ? N10 SPM 1203 A 1 
HETATM 11 C C11 SPM . . . D 4 131.887 159.107 123.529 1 44.09 ? C11 SPM 1203 A 1 
HETATM 12 C C12 SPM . . . D 4 130.418 159.098 123.95 1 44.09 ? C12 SPM 1203 A 1 
HETATM 13 C C13 SPM . . . D 4 129.863 160.513 123.81 1 44.09 ? C13 SPM 1203 A 1 
HETATM 14 N N14 SPM . . . D 4 128.396 160.464 123.763 1 44.09 ? N14 SPM 1203 A 1 
HETATM 15 H HN11 SPM . . . D 4 139.067 151.724 130.576 1 44.09 ? HN11 SPM 1203 A 1 
HETATM 16 H HN12 SPM . . . D 4 138.543 152.872 131.589 1 44.09 ? HN12 SPM 1203 A 1 
HETATM 17 H H21 SPM . . . D 4 139.861 153.869 130.002 1 44.09 ? H21 SPM 1203 A 1 
HETATM 18 H H22 SPM . . . D 4 138.902 153.103 128.714 1 44.09 ? H22 SPM 1203 A 1 
HETATM 19 H H31 SPM . . . D 4 137.174 154.554 130.547 1 44.09 ? H31 SPM 1203 A 1 
HETATM 20 H H32 SPM . . . D 4 138.437 155.621 129.884 1 44.09 ? H32 SPM 1203 A 1 
HETATM 21 H H41 SPM . . . D 4 137.882 154.875 127.601 1 44.09 ? H41 SPM 1203 A 1 
HETATM 22 H H42 SPM . . . D 4 136.649 153.772 128.248 1 44.09 ? H42 SPM 1203 A 1 
HETATM 23 H HN5 SPM . . . D 4 135.538 155.632 129.153 1 44.09 ? HN5 SPM 1203 A 1 
HETATM 24 H H61 SPM . . . D 4 136.118 155.617 126.319 1 44.09 ? H61 SPM 1203 A 1 
HETATM 25 H H62 SPM . . . D 4 134.874 154.697 127.198 1 44.09 ? H62 SPM 1203 A 1 
HETATM 26 H H71 SPM . . . D 4 133.64 156.719 127.699 1 44.09 ? H71 SPM 1203 A 1 
HETATM 27 H H72 SPM . . . D 4 134.954 157.737 127.06 1 44.09 ? H72 SPM 1203 A 1 
HETATM 28 H H81 SPM . . . D 4 134.647 156.636 124.822 1 44.09 ? H81 SPM 1203 A 1 
HETATM 29 H H82 SPM . . . D 4 133.262 155.74 125.483 1 44.09 ? H82 SPM 1203 A 1 
HETATM 30 H H91 SPM . . . D 4 132.055 157.801 125.905 1 44.09 ? H91 SPM 1203 A 1 
HETATM 31 H H92 SPM . . . D 4 133.48 158.772 125.47 1 44.09 ? H92 SPM 1203 A 1 
HETATM 32 H HN0 SPM . . . D 4 131.808 157.115 123.778 1 44.09 ? HN0 SPM 1203 A 1 
HETATM 33 H H111 SPM . . . D 4 132.401 159.921 124.041 1 44.09 ? H111 SPM 1203 A 1 
HETATM 34 H H112 SPM . . . D 4 131.946 159.272 122.454 1 44.09 ? H112 SPM 1203 A 1 
HETATM 35 H H121 SPM . . . D 4 129.859 158.417 123.308 1 44.09 ? H121 SPM 1203 A 1 
HETATM 36 H H122 SPM . . . D 4 130.33 158.776 124.987 1 44.09 ? H122 SPM 1203 A 1 
HETATM 37 H H131 SPM . . . D 4 130.18 161.112 124.661 1 44.09 ? H131 SPM 1203 A 1 
HETATM 38 H H132 SPM . . . D 4 130.242 160.959 122.89 1 44.09 ? H132 SPM 1203 A 1 
HETATM 39 H HN41 SPM . . . D 4 128.103 159.807 124.47 1 44.09 ? HN41 SPM 1203 A 1 
HETATM 40 H HN42 SPM . . . D 4 128.148 160.061 122.874 1 44.09 ? HN42 SPM 1203 A 1 
#
_model_server_stats.io_time_ms              9 
_model_server_stats.parse_time_ms           8 
_model_server_stats.create_model_time_ms    10 
_model_server_stats.query_time_ms           297 
_model_server_stats.encode_time_ms          1 
_model_server_stats.element_count           40 
#