data_7ZBG # _model_server_result.job_id hcnsE1jAE8Eyt8-3ziAOsA _model_server_result.datetime_utc '2025-06-28 04:58:57' _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 7zbg # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":507}' # _entry.id 7ZBG # _exptl.entry_id 7ZBG _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 284.312 _entity.id 5 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-[(2S,3R)-3-[3,5-bis(oxidanylidene)piperazin-1-ium-1-yl]butan-2-yl]piperazin-4-ium-2,6-dione _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 120 _cell.entry_id 7ZBG _cell.length_a 103.4 _cell.length_b 103.4 _cell.length_c 67.02 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 7ZBG _symmetry.cell_setting ? _symmetry.Int_Tables_number 150 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 3 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,D,E,F,G,H,I _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 'crystal symmetry operation' 4_555 y,x,-z -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 0 # _struct_asym.details ? _struct_asym.entity_id 5 _struct_asym.id H _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 OD1 ASN 63 A ASN 107 1_555 G MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.065 ? metalc ? metalc2 B O1B ADP . A ADP 501 1_555 G MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc3 B O1A ADP . A ADP 501 1_555 G MG MG . A MG 506 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.948 ? metalc ? metalc4 G MG MG . A MG 506 1_555 I O HOH . A HOH 611 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.259 ? metalc ? metalc5 G MG MG . A MG 506 1_555 I O HOH . A HOH 613 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.927 ? metalc ? metalc6 G MG MG . A MG 506 1_555 I O HOH . A HOH 627 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.043 ? # _chem_comp.formula 'C12 H20 N4 O4 2' _chem_comp.formula_weight 284.312 _chem_comp.id ITH _chem_comp.mon_nstd_flag . _chem_comp.name 4-[(2S,3R)-3-[3,5-bis(oxidanylidene)piperazin-1-ium-1-yl]butan-2-yl]piperazin-4-ium-2,6-dione _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 O4 C11 ITH doub 217 n n N4 C11 ITH sing 218 n n N4 C10 ITH sing 219 n n C11 C12 ITH sing 220 n n O3 C10 ITH doub 221 n n C10 C9 ITH sing 222 n n C12 N3 ITH sing 223 n n C9 N3 ITH sing 224 n n N3 C2 ITH sing 225 n n C1 C2 ITH sing 226 n n C2 C3 ITH sing 227 n n C3 C4 ITH sing 228 n n C3 N1 ITH sing 229 n n N1 C5 ITH sing 230 n n N1 C8 ITH sing 231 n n C5 C6 ITH sing 232 n n C8 C7 ITH sing 233 n n C7 O2 ITH doub 234 n n C7 N2 ITH sing 235 n n C6 N2 ITH sing 236 n n C6 O1 ITH doub 237 n n C1 H1 ITH sing 238 n n C1 H2 ITH sing 239 n n C1 H3 ITH sing 240 n n C2 H4 ITH sing 241 n n C3 H5 ITH sing 242 n n C4 H7 ITH sing 243 n n C4 H8 ITH sing 244 n n C4 H6 ITH sing 245 n n N1 H19 ITH sing 246 n n C5 H10 ITH sing 247 n n C5 H9 ITH sing 248 n n N2 H11 ITH sing 249 n n C8 H12 ITH sing 250 n n C8 H13 ITH sing 251 n n N3 H20 ITH sing 252 n n C9 H14 ITH sing 253 n n C9 H15 ITH sing 254 n n N4 H16 ITH sing 255 n n C12 H18 ITH sing 256 n n C12 H17 ITH sing 257 n n # _atom_sites.entry_id 7ZBG _atom_sites.fract_transf_matrix[1][1] 0.009671 _atom_sites.fract_transf_matrix[1][2] 0.005584 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.011167 _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] 0.014921 _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 ADP A 1 501 501 ADP ADP . C 3 SO4 A 1 502 1 SO4 SO4 . D 3 SO4 A 1 503 2 SO4 SO4 . E 3 SO4 A 1 504 3 SO4 SO4 . F 3 SO4 A 1 505 4 SO4 SO4 . G 4 MG A 1 506 3 MG MG . H 5 ITH A 1 507 5 ITH 00Z . I 6 HOH A 1 601 10 HOH HOH . I 6 HOH A 2 602 32 HOH HOH . I 6 HOH A 3 603 6 HOH HOH . I 6 HOH A 4 604 41 HOH HOH . I 6 HOH A 5 605 34 HOH HOH . I 6 HOH A 6 606 49 HOH HOH . I 6 HOH A 7 607 14 HOH HOH . I 6 HOH A 8 608 43 HOH HOH . I 6 HOH A 9 609 31 HOH HOH . I 6 HOH A 10 610 39 HOH HOH . I 6 HOH A 11 611 50 HOH HOH . I 6 HOH A 12 612 4 HOH HOH . I 6 HOH A 13 613 46 HOH HOH . I 6 HOH A 14 614 21 HOH HOH . I 6 HOH A 15 615 23 HOH HOH . I 6 HOH A 16 616 22 HOH HOH . I 6 HOH A 17 617 33 HOH HOH . I 6 HOH A 18 618 18 HOH HOH . I 6 HOH A 19 619 15 HOH HOH . I 6 HOH A 20 620 12 HOH HOH . I 6 HOH A 21 621 30 HOH HOH . I 6 HOH A 22 622 9 HOH HOH . I 6 HOH A 23 623 8 HOH HOH . I 6 HOH A 24 624 3 HOH HOH . I 6 HOH A 25 625 20 HOH HOH . I 6 HOH A 26 626 44 HOH HOH . I 6 HOH A 27 627 47 HOH HOH . I 6 HOH A 28 628 25 HOH HOH . I 6 HOH A 29 629 11 HOH HOH . I 6 HOH A 30 630 40 HOH HOH . I 6 HOH A 31 631 48 HOH HOH . I 6 HOH A 32 632 2 HOH HOH . I 6 HOH A 33 633 17 HOH HOH . I 6 HOH A 34 634 1 HOH HOH . I 6 HOH A 35 635 42 HOH HOH . I 6 HOH A 36 636 38 HOH HOH . I 6 HOH A 37 637 7 HOH HOH . I 6 HOH A 38 638 45 HOH HOH . I 6 HOH A 39 639 19 HOH HOH . I 6 HOH A 40 640 16 HOH HOH . I 6 HOH A 41 641 13 HOH HOH . I 6 HOH A 42 642 29 HOH HOH . I 6 HOH A 43 643 5 HOH HOH . I 6 HOH A 44 644 28 HOH HOH . I 6 HOH A 45 645 26 HOH HOH . I 6 HOH A 46 646 24 HOH HOH . I 6 HOH A 47 647 37 HOH HOH . I 6 HOH A 48 648 36 HOH HOH . I 6 HOH A 49 649 27 HOH HOH . I 6 HOH A 50 650 35 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 C C1 ITH . . . H 5 -14.184 -23.502 -1.103 0.5 39.44 0 C1 ITH 507 A 1 HETATM 2 C C2 ITH . . . H 5 -14.116 -24.876 -0.487 0.5 42.83 0 C2 ITH 507 A 1 HETATM 3 C C3 ITH . . . H 5 -14.958 -25.114 0.832 0.5 46.08 0 C3 ITH 507 A 1 HETATM 4 C C4 ITH . . . H 5 -14.941 -26.587 1.219 0.5 42.86 0 C4 ITH 507 A 1 HETATM 5 N N1 ITH . . . H 5 -14.677 -24.24 2.007 0.5 45.33 0 N1 ITH 507 A 1 HETATM 6 C C5 ITH . . . H 5 -13.415 -24.455 2.757 0.5 45.46 0 C5 ITH 507 A 1 HETATM 7 C C6 ITH . . . H 5 -13.553 -24.923 4.179 0.5 45.45 0 C6 ITH 507 A 1 HETATM 8 O O1 ITH . . . H 5 -12.575 -25.318 4.79 0.5 42.37 0 O1 ITH 507 A 1 HETATM 9 N N2 ITH . . . H 5 -14.801 -24.92 4.765 0.5 45.68 0 N2 ITH 507 A 1 HETATM 10 C C7 ITH . . . H 5 -15.976 -24.631 4.121 0.5 47.52 0 C7 ITH 507 A 1 HETATM 11 O O2 ITH . . . H 5 -17.066 -24.965 4.561 0.5 48.95 0 O2 ITH 507 A 1 HETATM 12 C C8 ITH . . . H 5 -15.833 -23.846 2.859 0.5 43.53 0 C8 ITH 507 A 1 HETATM 13 N N3 ITH . . . H 5 -14.49 -25.787 -1.6 0.5 46.46 0 N3 ITH 507 A 1 HETATM 14 C C9 ITH . . . H 5 -13.443 -26.689 -2.121 0.5 44.83 0 C9 ITH 507 A 1 HETATM 15 C C10 ITH . . . H 5 -12.6 -26.105 -3.205 0.5 40.67 0 C10 ITH 507 A 1 HETATM 16 O O3 ITH . . . H 5 -11.505 -26.563 -3.449 0.5 37.03 0 O3 ITH 507 A 1 HETATM 17 N N4 ITH . . . H 5 -13.13 -25.072 -3.933 0.5 45.44 0 N4 ITH 507 A 1 HETATM 18 C C11 ITH . . . H 5 -14.316 -24.447 -3.636 0.5 48.68 0 C11 ITH 507 A 1 HETATM 19 O O4 ITH . . . H 5 -14.614 -23.36 -4.087 0.5 45.2 0 O4 ITH 507 A 1 HETATM 20 C C12 ITH . . . H 5 -15.227 -25.176 -2.709 0.5 48.09 0 C12 ITH 507 A 1 HETATM 21 H H1 ITH . . . H 5 -13.834 -23.535 -2.011 0.5 40.45 0 H1 ITH 507 A 1 HETATM 22 H H2 ITH . . . H 5 -13.653 -22.882 -0.574 0.5 40.45 0 H2 ITH 507 A 1 HETATM 23 H H3 ITH . . . H 5 -15.109 -23.2 -1.124 0.5 40.45 0 H3 ITH 507 A 1 HETATM 24 H H4 ITH . . . H 5 -13.166 -25.06 -0.272 0.5 43.42 0 H4 ITH 507 A 1 HETATM 25 H H5 ITH . . . H 5 -15.897 -24.907 0.596 0.5 44.68 0 H5 ITH 507 A 1 HETATM 26 H H7 ITH . . . H 5 -14.134 -26.779 1.727 0.5 43.77 0 H7 ITH 507 A 1 HETATM 27 H H8 ITH . . . H 5 -14.956 -27.135 0.415 0.5 43.79 0 H8 ITH 507 A 1 HETATM 28 H H6 ITH . . . H 5 -15.722 -26.789 1.763 0.5 43.81 0 H6 ITH 507 A 1 HETATM 29 H H10 ITH . . . H 5 -12.907 -23.63 2.761 0.5 45.43 0 H10 ITH 507 A 1 HETATM 30 H H9 ITH . . . H 5 -12.882 -25.113 2.284 0.5 45.43 0 H9 ITH 507 A 1 HETATM 31 H H11 ITH . . . H 5 -14.843 -25.12 5.613 0.5 46.05 0 H11 ITH 507 A 1 HETATM 32 H H12 ITH . . . H 5 -16.653 -23.94 2.35 0.5 44.86 0 H12 ITH 507 A 1 HETATM 33 H H13 ITH . . . H 5 -15.742 -22.912 3.102 0.5 44.86 0 H13 ITH 507 A 1 HETATM 34 H H14 ITH . . . H 5 -12.859 -26.947 -1.392 0.5 44.12 0 H14 ITH 507 A 1 HETATM 35 H H15 ITH . . . H 5 -13.858 -27.493 -2.466 0.5 44.29 0 H15 ITH 507 A 1 HETATM 36 H H16 ITH . . . H 5 -12.702 -24.82 -4.653 0.5 44.92 0 H16 ITH 507 A 1 HETATM 37 H H18 ITH . . . H 5 -15.69 -25.865 -3.21 0.5 47.83 0 H18 ITH 507 A 1 HETATM 38 H H17 ITH . . . H 5 -15.883 -24.551 -2.362 0.5 47.83 0 H17 ITH 507 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 6 _model_server_stats.query_time_ms 251 _model_server_stats.encode_time_ms 3 _model_server_stats.element_count 38 #