data_8XJB # _model_server_result.job_id w2dhi4eb4VkjSQF5n_lwfg _model_server_result.datetime_utc '2025-01-11 17:48:57' _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 8xjb # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":500}' # _entry.id 8XJB # _exptl.entry_id 8XJB _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 1 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 113.64 _cell.angle_gamma 90 _cell.entry_id 8XJB _cell.length_a 73.73 _cell.length_b 54.89 _cell.length_c 51.91 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8XJB _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _pdbx_struct_assembly.details author_and_software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'point symmetry operation' ? ? -1 0 0 0 1 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _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 290 n n N1 HN11 SPM sing 291 n n N1 HN12 SPM sing 292 n n C2 C3 SPM sing 293 n n C2 H21 SPM sing 294 n n C2 H22 SPM sing 295 n n C3 C4 SPM sing 296 n n C3 H31 SPM sing 297 n n C3 H32 SPM sing 298 n n C4 N5 SPM sing 299 n n C4 H41 SPM sing 300 n n C4 H42 SPM sing 301 n n N5 C6 SPM sing 302 n n N5 HN5 SPM sing 303 n n C6 C7 SPM sing 304 n n C6 H61 SPM sing 305 n n C6 H62 SPM sing 306 n n C7 C8 SPM sing 307 n n C7 H71 SPM sing 308 n n C7 H72 SPM sing 309 n n C8 C9 SPM sing 310 n n C8 H81 SPM sing 311 n n C8 H82 SPM sing 312 n n C9 N10 SPM sing 313 n n C9 H91 SPM sing 314 n n C9 H92 SPM sing 315 n n N10 C11 SPM sing 316 n n N10 HN0 SPM sing 317 n n C11 C12 SPM sing 318 n n C11 H111 SPM sing 319 n n C11 H112 SPM sing 320 n n C12 C13 SPM sing 321 n n C12 H121 SPM sing 322 n n C12 H122 SPM sing 323 n n C13 N14 SPM sing 324 n n C13 H131 SPM sing 325 n n C13 H132 SPM sing 326 n n N14 HN41 SPM sing 327 n n N14 HN42 SPM sing 328 n n # _atom_sites.entry_id 8XJB _atom_sites.fract_transf_matrix[1][1] 0.013563 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.005937 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018218 _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] 0.021029 _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 SPM A 1 500 500 SPM SPM . C 3 HOH A 1 601 602 HOH HOH . C 3 HOH A 2 602 603 HOH HOH . C 3 HOH A 3 603 604 HOH HOH . C 3 HOH A 4 604 605 HOH HOH . C 3 HOH A 5 605 606 HOH HOH . C 3 HOH A 6 606 607 HOH HOH . C 3 HOH A 7 607 608 HOH HOH . C 3 HOH A 8 608 609 HOH HOH . C 3 HOH A 9 609 610 HOH HOH . C 3 HOH A 10 610 611 HOH HOH . C 3 HOH A 11 611 612 HOH HOH . C 3 HOH A 12 612 613 HOH HOH . C 3 HOH A 13 613 614 HOH HOH . C 3 HOH A 14 614 615 HOH HOH . C 3 HOH A 15 615 616 HOH HOH . C 3 HOH A 16 616 617 HOH HOH . C 3 HOH A 17 617 618 HOH HOH . C 3 HOH A 18 618 619 HOH HOH . C 3 HOH A 19 619 620 HOH HOH . C 3 HOH A 20 620 621 HOH HOH . C 3 HOH A 21 621 622 HOH HOH . C 3 HOH A 22 622 623 HOH HOH . C 3 HOH A 23 623 624 HOH HOH . C 3 HOH A 24 624 625 HOH HOH . C 3 HOH A 25 625 626 HOH HOH . C 3 HOH A 26 626 627 HOH HOH . C 3 HOH A 27 627 628 HOH HOH . C 3 HOH A 28 628 629 HOH HOH . C 3 HOH A 29 629 630 HOH HOH . C 3 HOH A 30 630 631 HOH HOH . C 3 HOH A 31 631 632 HOH HOH . C 3 HOH A 32 632 633 HOH HOH . C 3 HOH A 33 633 634 HOH HOH . C 3 HOH A 34 634 635 HOH HOH . C 3 HOH A 35 635 636 HOH HOH . C 3 HOH A 36 636 637 HOH HOH . C 3 HOH A 37 637 638 HOH HOH . C 3 HOH A 38 638 639 HOH HOH . C 3 HOH A 39 639 640 HOH HOH . C 3 HOH A 40 640 641 HOH HOH . C 3 HOH A 41 641 642 HOH HOH . C 3 HOH A 42 642 643 HOH HOH . C 3 HOH A 43 643 644 HOH HOH . C 3 HOH A 44 644 645 HOH HOH . C 3 HOH A 45 645 646 HOH HOH . C 3 HOH A 46 646 647 HOH HOH . C 3 HOH A 47 647 648 HOH HOH . C 3 HOH A 48 648 649 HOH HOH . C 3 HOH A 49 649 650 HOH HOH . C 3 HOH A 50 650 651 HOH HOH . C 3 HOH A 51 651 652 HOH HOH . C 3 HOH A 52 652 653 HOH HOH . C 3 HOH A 53 653 654 HOH HOH . C 3 HOH A 54 654 655 HOH HOH . C 3 HOH A 55 655 656 HOH HOH . C 3 HOH A 56 656 657 HOH HOH . C 3 HOH A 57 657 658 HOH HOH . C 3 HOH A 58 658 659 HOH HOH . C 3 HOH A 59 659 660 HOH HOH . C 3 HOH A 60 660 661 HOH HOH . C 3 HOH A 61 661 662 HOH HOH . C 3 HOH A 62 662 663 HOH HOH . C 3 HOH A 63 663 664 HOH HOH . C 3 HOH A 64 664 665 HOH HOH . C 3 HOH A 65 665 666 HOH HOH . C 3 HOH A 66 666 667 HOH HOH . C 3 HOH A 67 667 669 HOH HOH . C 3 HOH A 68 668 670 HOH HOH . C 3 HOH A 69 669 671 HOH HOH . C 3 HOH A 70 670 672 HOH HOH . C 3 HOH A 71 671 673 HOH HOH . C 3 HOH A 72 672 674 HOH HOH . C 3 HOH A 73 673 675 HOH HOH . C 3 HOH A 74 674 676 HOH HOH . C 3 HOH A 75 675 677 HOH HOH . C 3 HOH A 76 676 678 HOH HOH . C 3 HOH A 77 677 679 HOH HOH . C 3 HOH A 78 678 680 HOH HOH . C 3 HOH A 79 679 681 HOH HOH . C 3 HOH A 80 680 682 HOH HOH . C 3 HOH A 81 681 683 HOH HOH . C 3 HOH A 82 682 684 HOH HOH . C 3 HOH A 83 683 685 HOH HOH . C 3 HOH A 84 684 686 HOH HOH . C 3 HOH A 85 685 687 HOH HOH . C 3 HOH A 86 686 688 HOH HOH . C 3 HOH A 87 687 689 HOH HOH . C 3 HOH A 88 688 690 HOH HOH . C 3 HOH A 89 689 692 HOH HOH . C 3 HOH A 90 690 693 HOH HOH . C 3 HOH A 91 691 694 HOH HOH . C 3 HOH A 92 692 695 HOH HOH . C 3 HOH A 93 693 696 HOH HOH . C 3 HOH A 94 694 697 HOH HOH . C 3 HOH A 95 695 698 HOH HOH . C 3 HOH A 96 696 699 HOH HOH . C 3 HOH A 97 697 700 HOH HOH . C 3 HOH A 98 698 701 HOH HOH . C 3 HOH A 99 699 702 HOH HOH . C 3 HOH A 100 700 703 HOH HOH . C 3 HOH A 101 701 704 HOH HOH . C 3 HOH A 102 702 705 HOH HOH . C 3 HOH A 103 703 706 HOH HOH . C 3 HOH A 104 704 707 HOH HOH . C 3 HOH A 105 705 708 HOH HOH . C 3 HOH A 106 706 709 HOH HOH . C 3 HOH A 107 707 710 HOH HOH . C 3 HOH A 108 708 711 HOH HOH . C 3 HOH A 109 709 712 HOH HOH . C 3 HOH A 110 710 713 HOH HOH . C 3 HOH A 111 711 714 HOH HOH . C 3 HOH A 112 712 715 HOH HOH . C 3 HOH A 113 713 716 HOH HOH . C 3 HOH A 114 714 717 HOH HOH . C 3 HOH A 115 715 718 HOH HOH . C 3 HOH A 116 716 719 HOH HOH . C 3 HOH A 117 717 720 HOH HOH . C 3 HOH A 118 718 721 HOH HOH . C 3 HOH A 119 719 722 HOH HOH . C 3 HOH A 120 720 723 HOH HOH . C 3 HOH A 121 721 724 HOH HOH . C 3 HOH A 122 722 725 HOH HOH . C 3 HOH A 123 723 727 HOH HOH . C 3 HOH A 124 724 728 HOH HOH . C 3 HOH A 125 725 730 HOH HOH . C 3 HOH A 126 726 731 HOH HOH . C 3 HOH A 127 727 732 HOH HOH . C 3 HOH A 128 728 733 HOH HOH . C 3 HOH A 129 729 734 HOH HOH . C 3 HOH A 130 730 735 HOH HOH . C 3 HOH A 131 731 736 HOH HOH . C 3 HOH A 132 732 737 HOH HOH . C 3 HOH A 133 733 738 HOH HOH . C 3 HOH A 134 734 739 HOH HOH . C 3 HOH A 135 735 740 HOH HOH . C 3 HOH A 136 736 741 HOH HOH . C 3 HOH A 137 737 742 HOH HOH . C 3 HOH A 138 738 743 HOH HOH . C 3 HOH A 139 739 744 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 . . . B 2 -3.393 7.834 12.975 1 51.64 ? N1 SPM 500 A 1 HETATM 2 C C2 SPM . . . B 2 -4.36 8.143 11.941 1 51.39 ? C2 SPM 500 A 1 HETATM 3 C C3 SPM . . . B 2 -3.86 9.278 11.062 1 50.32 ? C3 SPM 500 A 1 HETATM 4 C C4 SPM . . . B 2 -2.417 9.622 11.4 1 49.86 ? C4 SPM 500 A 1 HETATM 5 N N5 SPM . . . B 2 -1.59 9.742 10.216 1 48.87 ? N5 SPM 500 A 1 HETATM 6 C C6 SPM . . . B 2 -0.311 10.406 10.345 1 47.86 ? C6 SPM 500 A 1 HETATM 7 C C7 SPM . . . B 2 0.36 10.619 8.999 1 47.74 ? C7 SPM 500 A 1 HETATM 8 C C8 SPM . . . B 2 1.813 11.038 9.187 1 47.56 ? C8 SPM 500 A 1 HETATM 9 C C9 SPM . . . B 2 2.7 9.835 9.49 1 48.02 ? C9 SPM 500 A 1 HETATM 10 N N10 SPM . . . B 2 4.107 10.122 9.29 1 52.35 ? N10 SPM 500 A 1 HETATM 11 C C11 SPM . . . B 2 5.101 9.097 9.537 1 58.09 ? C11 SPM 500 A 1 HETATM 12 C C12 SPM . . . B 2 6.343 9.676 10.204 1 64.72 ? C12 SPM 500 A 1 HETATM 13 C C13 SPM . . . B 2 5.979 10.736 11.24 1 70.97 ? C13 SPM 500 A 1 HETATM 14 N N14 SPM . . . B 2 5.293 10.154 12.377 1 77.46 ? N14 SPM 500 A 1 # _model_server_stats.io_time_ms 49 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 277 _model_server_stats.encode_time_ms 15 _model_server_stats.element_count 14 #