data_1XPQ # _model_server_result.job_id 56aFiNrrx7ejIc7JwERIWw _model_server_result.datetime_utc '2025-01-10 16:43:49' _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 1xpq # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":601}' # _entry.id 1XPQ # _exptl.entry_id 1XPQ _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 103.28 _cell.angle_gamma 90 _cell.entry_id 1XPQ _cell.length_a 103.048 _cell.length_b 98.133 _cell.length_c 123.832 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1XPQ _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 software_defined_assembly 1 PISA dimeric 2 software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,M,N 1 1 C,D,I,J,K,L,O,P 2 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 E N N ? 2 G N N ? 2 I N N ? 2 K 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 disulf ? disulf1 A SG CYS 221 A CYS 221 1_555 A SG CYS 238 A CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.068 ? disulf ? disulf2 B SG CYS 221 B CYS 221 1_555 B SG CYS 238 B CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? disulf ? disulf3 C SG CYS 221 C CYS 221 1_555 C SG CYS 238 C CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? disulf ? disulf4 D SG CYS 221 D CYS 221 1_555 D SG CYS 238 D CYS 238 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.063 ? # _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 381 n n N1 HN11 SPM sing 382 n n N1 HN12 SPM sing 383 n n C2 C3 SPM sing 384 n n C2 H21 SPM sing 385 n n C2 H22 SPM sing 386 n n C3 C4 SPM sing 387 n n C3 H31 SPM sing 388 n n C3 H32 SPM sing 389 n n C4 N5 SPM sing 390 n n C4 H41 SPM sing 391 n n C4 H42 SPM sing 392 n n N5 C6 SPM sing 393 n n N5 HN5 SPM sing 394 n n C6 C7 SPM sing 395 n n C6 H61 SPM sing 396 n n C6 H62 SPM sing 397 n n C7 C8 SPM sing 398 n n C7 H71 SPM sing 399 n n C7 H72 SPM sing 400 n n C8 C9 SPM sing 401 n n C8 H81 SPM sing 402 n n C8 H82 SPM sing 403 n n C9 N10 SPM sing 404 n n C9 H91 SPM sing 405 n n C9 H92 SPM sing 406 n n N10 C11 SPM sing 407 n n N10 HN0 SPM sing 408 n n C11 C12 SPM sing 409 n n C11 H111 SPM sing 410 n n C11 H112 SPM sing 411 n n C12 C13 SPM sing 412 n n C12 H121 SPM sing 413 n n C12 H122 SPM sing 414 n n C13 N14 SPM sing 415 n n C13 H131 SPM sing 416 n n C13 H132 SPM sing 417 n n N14 HN41 SPM sing 418 n n N14 HN42 SPM sing 419 n n # _atom_sites.entry_id 1XPQ _atom_sites.fract_transf_matrix[1][1] 0.009704 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00229 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01019 _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] 0.008297 _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 E 2 SPM A 1 601 924 SPM SPM . F 3 FAD A 1 602 803 FAD FAD . G 2 SPM B 1 601 923 SPM SPM . H 3 FAD B 1 602 804 FAD FAD . I 2 SPM C 1 601 921 SPM SPM . J 3 FAD C 1 602 801 FAD FAD . K 2 SPM D 1 601 922 SPM SPM . L 3 FAD D 1 602 802 FAD FAD . M 4 HOH A 1 701 1 HOH HOH . M 4 HOH A 2 702 191 HOH HOH . M 4 HOH A 3 703 184 HOH HOH . M 4 HOH A 4 704 19 HOH HOH . M 4 HOH A 5 705 146 HOH HOH . M 4 HOH A 6 706 178 HOH HOH . M 4 HOH A 7 707 154 HOH HOH . M 4 HOH A 8 708 145 HOH HOH . M 4 HOH A 9 709 103 HOH HOH . M 4 HOH A 10 710 150 HOH HOH . M 4 HOH A 11 711 112 HOH HOH . M 4 HOH A 12 712 14 HOH HOH . M 4 HOH A 13 713 116 HOH HOH . M 4 HOH A 14 714 8 HOH HOH . M 4 HOH A 15 715 10 HOH HOH . M 4 HOH A 16 716 223 HOH HOH . M 4 HOH A 17 717 163 HOH HOH . M 4 HOH A 18 718 15 HOH HOH . M 4 HOH A 19 719 227 HOH HOH . M 4 HOH A 20 720 177 HOH HOH . M 4 HOH A 21 721 5 HOH HOH . M 4 HOH A 22 722 9 HOH HOH . M 4 HOH A 23 723 182 HOH HOH . M 4 HOH A 24 724 21 HOH HOH . M 4 HOH A 25 725 6 HOH HOH . M 4 HOH A 26 726 173 HOH HOH . M 4 HOH A 27 727 3 HOH HOH . M 4 HOH A 28 728 17 HOH HOH . M 4 HOH A 29 729 13 HOH HOH . M 4 HOH A 30 730 126 HOH HOH . M 4 HOH A 31 731 195 HOH HOH . M 4 HOH A 32 732 12 HOH HOH . M 4 HOH A 33 733 214 HOH HOH . M 4 HOH A 34 734 228 HOH HOH . M 4 HOH A 35 735 110 HOH HOH . M 4 HOH A 36 736 206 HOH HOH . M 4 HOH A 37 737 11 HOH HOH . M 4 HOH A 38 738 221 HOH HOH . M 4 HOH A 39 739 22 HOH HOH . M 4 HOH A 40 740 187 HOH HOH . M 4 HOH A 41 741 152 HOH HOH . M 4 HOH A 42 742 157 HOH HOH . M 4 HOH A 43 743 4 HOH HOH . M 4 HOH A 44 744 20 HOH HOH . M 4 HOH A 45 745 2 HOH HOH . M 4 HOH A 46 746 234 HOH HOH . M 4 HOH A 47 747 193 HOH HOH . M 4 HOH A 48 748 7 HOH HOH . M 4 HOH A 49 749 218 HOH HOH . M 4 HOH A 50 750 97 HOH HOH . M 4 HOH A 51 751 105 HOH HOH . M 4 HOH A 52 752 232 HOH HOH . M 4 HOH A 53 753 142 HOH HOH . M 4 HOH A 54 754 18 HOH HOH . M 4 HOH A 55 755 220 HOH HOH . M 4 HOH A 56 756 203 HOH HOH . M 4 HOH A 57 757 170 HOH HOH . M 4 HOH A 58 758 155 HOH HOH . M 4 HOH A 59 759 16 HOH HOH . M 4 HOH A 60 760 171 HOH HOH . N 4 HOH B 1 701 199 HOH HOH . N 4 HOH B 2 702 115 HOH HOH . N 4 HOH B 3 703 29 HOH HOH . N 4 HOH B 4 704 148 HOH HOH . N 4 HOH B 5 705 219 HOH HOH . N 4 HOH B 6 706 197 HOH HOH . N 4 HOH B 7 707 133 HOH HOH . N 4 HOH B 8 708 175 HOH HOH . N 4 HOH B 9 709 132 HOH HOH . N 4 HOH B 10 710 217 HOH HOH . N 4 HOH B 11 711 23 HOH HOH . N 4 HOH B 12 712 28 HOH HOH . N 4 HOH B 13 713 120 HOH HOH . N 4 HOH B 14 714 30 HOH HOH . N 4 HOH B 15 715 24 HOH HOH . N 4 HOH B 16 716 26 HOH HOH . N 4 HOH B 17 717 198 HOH HOH . N 4 HOH B 18 718 25 HOH HOH . N 4 HOH B 19 719 102 HOH HOH . N 4 HOH B 20 720 172 HOH HOH . N 4 HOH B 21 721 127 HOH HOH . N 4 HOH B 22 722 36 HOH HOH . N 4 HOH B 23 723 186 HOH HOH . N 4 HOH B 24 724 165 HOH HOH . N 4 HOH B 25 725 202 HOH HOH . N 4 HOH B 26 726 118 HOH HOH . N 4 HOH B 27 727 34 HOH HOH . N 4 HOH B 28 728 31 HOH HOH . N 4 HOH B 29 729 212 HOH HOH . N 4 HOH B 30 730 33 HOH HOH . N 4 HOH B 31 731 35 HOH HOH . N 4 HOH B 32 732 231 HOH HOH . N 4 HOH B 33 733 216 HOH HOH . N 4 HOH B 34 734 27 HOH HOH . N 4 HOH B 35 735 209 HOH HOH . N 4 HOH B 36 736 32 HOH HOH . N 4 HOH B 37 737 156 HOH HOH . N 4 HOH B 38 738 38 HOH HOH . N 4 HOH B 39 739 136 HOH HOH . N 4 HOH B 40 740 37 HOH HOH . N 4 HOH B 41 741 226 HOH HOH . N 4 HOH B 42 742 134 HOH HOH . N 4 HOH B 43 743 174 HOH HOH . N 4 HOH B 44 744 100 HOH HOH . N 4 HOH B 45 745 230 HOH HOH . N 4 HOH B 46 746 180 HOH HOH . O 4 HOH C 1 701 160 HOH HOH . O 4 HOH C 2 702 153 HOH HOH . O 4 HOH C 3 703 135 HOH HOH . O 4 HOH C 4 704 62 HOH HOH . O 4 HOH C 5 705 229 HOH HOH . O 4 HOH C 6 706 65 HOH HOH . O 4 HOH C 7 707 169 HOH HOH . O 4 HOH C 8 708 123 HOH HOH . O 4 HOH C 9 709 104 HOH HOH . O 4 HOH C 10 710 167 HOH HOH . O 4 HOH C 11 711 121 HOH HOH . O 4 HOH C 12 712 68 HOH HOH . O 4 HOH C 13 713 107 HOH HOH . O 4 HOH C 14 714 58 HOH HOH . O 4 HOH C 15 715 114 HOH HOH . O 4 HOH C 16 716 149 HOH HOH . O 4 HOH C 17 717 47 HOH HOH . O 4 HOH C 18 718 71 HOH HOH . O 4 HOH C 19 719 72 HOH HOH . O 4 HOH C 20 720 43 HOH HOH . O 4 HOH C 21 721 50 HOH HOH . O 4 HOH C 22 722 55 HOH HOH . O 4 HOH C 23 723 45 HOH HOH . O 4 HOH C 24 724 42 HOH HOH . O 4 HOH C 25 725 101 HOH HOH . O 4 HOH C 26 726 53 HOH HOH . O 4 HOH C 27 727 60 HOH HOH . O 4 HOH C 28 728 49 HOH HOH . O 4 HOH C 29 729 57 HOH HOH . O 4 HOH C 30 730 48 HOH HOH . O 4 HOH C 31 731 46 HOH HOH . O 4 HOH C 32 732 201 HOH HOH . O 4 HOH C 33 733 56 HOH HOH . O 4 HOH C 34 734 181 HOH HOH . O 4 HOH C 35 735 192 HOH HOH . O 4 HOH C 36 736 139 HOH HOH . O 4 HOH C 37 737 40 HOH HOH . O 4 HOH C 38 738 211 HOH HOH . O 4 HOH C 39 739 59 HOH HOH . O 4 HOH C 40 740 129 HOH HOH . O 4 HOH C 41 741 215 HOH HOH . O 4 HOH C 42 742 63 HOH HOH . O 4 HOH C 43 743 66 HOH HOH . O 4 HOH C 44 744 52 HOH HOH . O 4 HOH C 45 745 41 HOH HOH . O 4 HOH C 46 746 44 HOH HOH . O 4 HOH C 47 747 190 HOH HOH . O 4 HOH C 48 748 166 HOH HOH . O 4 HOH C 49 749 122 HOH HOH . O 4 HOH C 50 750 61 HOH HOH . O 4 HOH C 51 751 39 HOH HOH . O 4 HOH C 52 752 67 HOH HOH . O 4 HOH C 53 753 54 HOH HOH . O 4 HOH C 54 754 51 HOH HOH . O 4 HOH C 55 755 95 HOH HOH . O 4 HOH C 56 756 125 HOH HOH . O 4 HOH C 57 757 98 HOH HOH . O 4 HOH C 58 758 144 HOH HOH . O 4 HOH C 59 759 200 HOH HOH . O 4 HOH C 60 760 131 HOH HOH . O 4 HOH C 61 761 64 HOH HOH . O 4 HOH C 62 762 143 HOH HOH . O 4 HOH C 63 763 205 HOH HOH . O 4 HOH C 64 764 140 HOH HOH . O 4 HOH C 65 765 233 HOH HOH . O 4 HOH C 66 766 69 HOH HOH . O 4 HOH C 67 767 70 HOH HOH . O 4 HOH C 68 768 168 HOH HOH . O 4 HOH C 69 769 161 HOH HOH . O 4 HOH C 70 770 113 HOH HOH . O 4 HOH C 71 771 111 HOH HOH . O 4 HOH C 72 772 151 HOH HOH . O 4 HOH C 73 773 106 HOH HOH . P 4 HOH D 1 701 207 HOH HOH . P 4 HOH D 2 702 158 HOH HOH . P 4 HOH D 3 703 78 HOH HOH . P 4 HOH D 4 704 117 HOH HOH . P 4 HOH D 5 705 128 HOH HOH . P 4 HOH D 6 706 76 HOH HOH . P 4 HOH D 7 707 93 HOH HOH . P 4 HOH D 8 708 82 HOH HOH . P 4 HOH D 9 709 81 HOH HOH . P 4 HOH D 10 710 88 HOH HOH . P 4 HOH D 11 711 204 HOH HOH . P 4 HOH D 12 712 185 HOH HOH . P 4 HOH D 13 713 137 HOH HOH . P 4 HOH D 14 714 87 HOH HOH . P 4 HOH D 15 715 119 HOH HOH . P 4 HOH D 16 716 109 HOH HOH . P 4 HOH D 17 717 75 HOH HOH . P 4 HOH D 18 718 79 HOH HOH . P 4 HOH D 19 719 90 HOH HOH . P 4 HOH D 20 720 130 HOH HOH . P 4 HOH D 21 721 84 HOH HOH . P 4 HOH D 22 722 86 HOH HOH . P 4 HOH D 23 723 94 HOH HOH . P 4 HOH D 24 724 222 HOH HOH . P 4 HOH D 25 725 89 HOH HOH . P 4 HOH D 26 726 80 HOH HOH . P 4 HOH D 27 727 225 HOH HOH . P 4 HOH D 28 728 210 HOH HOH . P 4 HOH D 29 729 162 HOH HOH . P 4 HOH D 30 730 194 HOH HOH . P 4 HOH D 31 731 124 HOH HOH . P 4 HOH D 32 732 73 HOH HOH . P 4 HOH D 33 733 83 HOH HOH . P 4 HOH D 34 734 224 HOH HOH . P 4 HOH D 35 735 138 HOH HOH . P 4 HOH D 36 736 188 HOH HOH . P 4 HOH D 37 737 141 HOH HOH . P 4 HOH D 38 738 213 HOH HOH . P 4 HOH D 39 739 85 HOH HOH . P 4 HOH D 40 740 108 HOH HOH . P 4 HOH D 41 741 99 HOH HOH . P 4 HOH D 42 742 235 HOH HOH . P 4 HOH D 43 743 164 HOH HOH . P 4 HOH D 44 744 147 HOH HOH . P 4 HOH D 45 745 77 HOH HOH . P 4 HOH D 46 746 189 HOH HOH . P 4 HOH D 47 747 179 HOH HOH . P 4 HOH D 48 748 74 HOH HOH . P 4 HOH D 49 749 92 HOH HOH . P 4 HOH D 50 750 176 HOH HOH . P 4 HOH D 51 751 159 HOH HOH . P 4 HOH D 52 752 96 HOH HOH . P 4 HOH D 53 753 91 HOH HOH . P 4 HOH D 54 754 183 HOH HOH . P 4 HOH D 55 755 196 HOH HOH . P 4 HOH D 56 756 208 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 . . . E 2 23.14 3.671 8.924 1 60.99 ? N1 SPM 601 A 1 HETATM 2 C C2 SPM . . . E 2 24.281 3.187 9.407 1 61.54 ? C2 SPM 601 A 1 HETATM 3 C C3 SPM . . . E 2 24.672 3.454 10.724 1 62.37 ? C3 SPM 601 A 1 HETATM 4 C C4 SPM . . . E 2 25.965 3.214 11.188 1 53.75 ? C4 SPM 601 A 1 HETATM 5 N N5 SPM . . . E 2 26.12 2.584 12.341 1 49.44 ? N5 SPM 601 A 1 HETATM 6 C C6 SPM . . . E 2 26.381 1.294 12.156 1 48.17 ? C6 SPM 601 A 1 HETATM 7 C C7 SPM . . . E 2 27.237 0.835 11.165 1 50.59 ? C7 SPM 601 A 1 HETATM 8 C C8 SPM . . . E 2 27.581 -0.511 11.111 1 53.54 ? C8 SPM 601 A 1 HETATM 9 C C9 SPM . . . E 2 28.411 -1.053 12.085 1 53.77 ? C9 SPM 601 A 1 HETATM 10 N N10 SPM . . . E 2 28.262 -2.311 12.478 1 61.31 ? N10 SPM 601 A 1 HETATM 11 C C11 SPM . . . E 2 28.338 -2.41 13.815 1 52.4 ? C11 SPM 601 A 1 HETATM 12 C C12 SPM . . . E 2 28.401 -3.657 14.454 1 47.43 ? C12 SPM 601 A 1 HETATM 13 C C13 SPM . . . E 2 27.3 -4.246 15.085 1 44.25 ? C13 SPM 601 A 1 HETATM 14 N N14 SPM . . . E 2 27.114 -5.564 15.043 1 50.69 ? N14 SPM 601 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 31 _model_server_stats.query_time_ms 340 _model_server_stats.encode_time_ms 13 _model_server_stats.element_count 14 #