data_8G9D # _model_server_result.job_id lVViMHY6SAf2HK0FXan5hA _model_server_result.datetime_utc '2025-07-24 04:49:47' _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 8g9d # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":401}' # _entry.id 8G9D # _exptl.entry_id 8G9D _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 737.068 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic acid' _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 8G9D _cell.length_a 46.444 _cell.length_b 59.711 _cell.length_c 62.402 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 8G9D _symmetry.cell_setting ? _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 PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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 # _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 2 _struct_asym.id B _struct_asym.pdbx_modified N _struct_asym.pdbx_blank_PDB_chainid_flag N # _chem_comp.formula 'C8 H19 F2 N O24 P6' _chem_comp.formula_weight 737.068 _chem_comp.id KDJ _chem_comp.mon_nstd_flag . _chem_comp.name '(1,1-difluoro-2-oxo-2-{[(1s,2R,3S,4s,5R,6S)-2,3,4,5,6-pentakis(phosphonooxy)cyclohexyl]amino}ethyl)phosphonic acid' _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 O32 PA2 KDJ doub 173 n n O42 PA2 KDJ sing 174 n n O41 PA1 KDJ doub 175 n n O31 PA1 KDJ sing 176 n n PA2 O22 KDJ sing 177 n n PA2 O12 KDJ sing 178 n n PA1 O11 KDJ sing 179 n n PA1 O21 KDJ sing 180 n n O11 C1 KDJ sing 181 n n O12 C2 KDJ sing 182 n n O46 PA6 KDJ doub 183 n n C2 C1 KDJ sing 184 n n C2 C3 KDJ sing 185 n n C1 C6 KDJ sing 186 n n O33 PA3 KDJ doub 187 n n O43 PA3 KDJ sing 188 n n O13 PA3 KDJ sing 189 n n O13 C3 KDJ sing 190 n n C6 O16 KDJ sing 191 n n C6 C5 KDJ sing 192 n n PA6 O36 KDJ sing 193 n n PA6 O16 KDJ sing 194 n n PA6 O26 KDJ sing 195 n n PA3 O23 KDJ sing 196 n n C3 C4 KDJ sing 197 n n C4 C5 KDJ sing 198 n n C4 O14 KDJ sing 199 n n O24 PA4 KDJ doub 200 n n C5 N15 KDJ sing 201 n n N15 C25 KDJ sing 202 n n O14 PA4 KDJ sing 203 n n PA4 O34 KDJ sing 204 n n PA4 O44 KDJ sing 205 n n O85 PB5 KDJ doub 206 n n C25 O35 KDJ doub 207 n n C25 C45 KDJ sing 208 n n F55 C45 KDJ sing 209 n n C45 PB5 KDJ sing 210 n n C45 F65 KDJ sing 211 n n PB5 O95 KDJ sing 212 n n PB5 O75 KDJ sing 213 n n N15 H1 KDJ sing 214 n n C3 H2 KDJ sing 215 n n C4 H3 KDJ sing 216 n n C5 H4 KDJ sing 217 n n C6 H5 KDJ sing 218 n n C1 H6 KDJ sing 219 n n C2 H7 KDJ sing 220 n n O75 H8 KDJ sing 221 n n O95 H9 KDJ sing 222 n n O34 H10 KDJ sing 223 n n O44 H11 KDJ sing 224 n n O43 H12 KDJ sing 225 n n O23 H13 KDJ sing 226 n n O42 H14 KDJ sing 227 n n O22 H15 KDJ sing 228 n n O31 H16 KDJ sing 229 n n O21 H17 KDJ sing 230 n n O36 H18 KDJ sing 231 n n O26 H19 KDJ sing 232 n n # _atom_sites.entry_id 8G9D _atom_sites.fract_transf_matrix[1][1] 0.021531 _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] 0.016747 _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] 0.016025 _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 KDJ A 1 401 401 KDJ KDJ . C 3 HOH A 1 501 120 HOH HOH . C 3 HOH A 2 502 91 HOH HOH . C 3 HOH A 3 503 131 HOH HOH . C 3 HOH A 4 504 130 HOH HOH . C 3 HOH A 5 505 96 HOH HOH . C 3 HOH A 6 506 60 HOH HOH . C 3 HOH A 7 507 132 HOH HOH . C 3 HOH A 8 508 124 HOH HOH . C 3 HOH A 9 509 74 HOH HOH . C 3 HOH A 10 510 118 HOH HOH . C 3 HOH A 11 511 68 HOH HOH . C 3 HOH A 12 512 106 HOH HOH . C 3 HOH A 13 513 109 HOH HOH . C 3 HOH A 14 514 113 HOH HOH . C 3 HOH A 15 515 98 HOH HOH . C 3 HOH A 16 516 84 HOH HOH . C 3 HOH A 17 517 31 HOH HOH . C 3 HOH A 18 518 76 HOH HOH . C 3 HOH A 19 519 104 HOH HOH . C 3 HOH A 20 520 6 HOH HOH . C 3 HOH A 21 521 97 HOH HOH . C 3 HOH A 22 522 107 HOH HOH . C 3 HOH A 23 523 90 HOH HOH . C 3 HOH A 24 524 127 HOH HOH . C 3 HOH A 25 525 125 HOH HOH . C 3 HOH A 26 526 92 HOH HOH . C 3 HOH A 27 527 123 HOH HOH . C 3 HOH A 28 528 75 HOH HOH . C 3 HOH A 29 529 1 HOH HOH . C 3 HOH A 30 530 45 HOH HOH . C 3 HOH A 31 531 3 HOH HOH . C 3 HOH A 32 532 28 HOH HOH . C 3 HOH A 33 533 27 HOH HOH . C 3 HOH A 34 534 47 HOH HOH . C 3 HOH A 35 535 35 HOH HOH . C 3 HOH A 36 536 128 HOH HOH . C 3 HOH A 37 537 67 HOH HOH . C 3 HOH A 38 538 23 HOH HOH . C 3 HOH A 39 539 63 HOH HOH . C 3 HOH A 40 540 77 HOH HOH . C 3 HOH A 41 541 19 HOH HOH . C 3 HOH A 42 542 7 HOH HOH . C 3 HOH A 43 543 42 HOH HOH . C 3 HOH A 44 544 102 HOH HOH . C 3 HOH A 45 545 2 HOH HOH . C 3 HOH A 46 546 64 HOH HOH . C 3 HOH A 47 547 21 HOH HOH . C 3 HOH A 48 548 83 HOH HOH . C 3 HOH A 49 549 56 HOH HOH . C 3 HOH A 50 550 73 HOH HOH . C 3 HOH A 51 551 58 HOH HOH . C 3 HOH A 52 552 22 HOH HOH . C 3 HOH A 53 553 13 HOH HOH . C 3 HOH A 54 554 111 HOH HOH . C 3 HOH A 55 555 94 HOH HOH . C 3 HOH A 56 556 54 HOH HOH . C 3 HOH A 57 557 44 HOH HOH . C 3 HOH A 58 558 69 HOH HOH . C 3 HOH A 59 559 100 HOH HOH . C 3 HOH A 60 560 15 HOH HOH . C 3 HOH A 61 561 61 HOH HOH . C 3 HOH A 62 562 55 HOH HOH . C 3 HOH A 63 563 10 HOH HOH . C 3 HOH A 64 564 25 HOH HOH . C 3 HOH A 65 565 59 HOH HOH . C 3 HOH A 66 566 105 HOH HOH . C 3 HOH A 67 567 14 HOH HOH . C 3 HOH A 68 568 9 HOH HOH . C 3 HOH A 69 569 49 HOH HOH . C 3 HOH A 70 570 85 HOH HOH . C 3 HOH A 71 571 18 HOH HOH . C 3 HOH A 72 572 93 HOH HOH . C 3 HOH A 73 573 36 HOH HOH . C 3 HOH A 74 574 11 HOH HOH . C 3 HOH A 75 575 8 HOH HOH . C 3 HOH A 76 576 70 HOH HOH . C 3 HOH A 77 577 72 HOH HOH . C 3 HOH A 78 578 5 HOH HOH . C 3 HOH A 79 579 50 HOH HOH . C 3 HOH A 80 580 16 HOH HOH . C 3 HOH A 81 581 82 HOH HOH . C 3 HOH A 82 582 78 HOH HOH . C 3 HOH A 83 583 34 HOH HOH . C 3 HOH A 84 584 17 HOH HOH . C 3 HOH A 85 585 37 HOH HOH . C 3 HOH A 86 586 89 HOH HOH . C 3 HOH A 87 587 41 HOH HOH . C 3 HOH A 88 588 57 HOH HOH . C 3 HOH A 89 589 40 HOH HOH . C 3 HOH A 90 590 79 HOH HOH . C 3 HOH A 91 591 26 HOH HOH . C 3 HOH A 92 592 24 HOH HOH . C 3 HOH A 93 593 101 HOH HOH . C 3 HOH A 94 594 29 HOH HOH . C 3 HOH A 95 595 103 HOH HOH . C 3 HOH A 96 596 88 HOH HOH . C 3 HOH A 97 597 95 HOH HOH . C 3 HOH A 98 598 4 HOH HOH . C 3 HOH A 99 599 99 HOH HOH . C 3 HOH A 100 600 20 HOH HOH . C 3 HOH A 101 601 108 HOH HOH . C 3 HOH A 102 602 65 HOH HOH . C 3 HOH A 103 603 62 HOH HOH . C 3 HOH A 104 604 87 HOH HOH . C 3 HOH A 105 605 12 HOH HOH . C 3 HOH A 106 606 134 HOH HOH . C 3 HOH A 107 607 129 HOH HOH . C 3 HOH A 108 608 119 HOH HOH . C 3 HOH A 109 609 121 HOH HOH . C 3 HOH A 110 610 122 HOH HOH . C 3 HOH A 111 611 39 HOH HOH . C 3 HOH A 112 612 114 HOH HOH . C 3 HOH A 113 613 86 HOH HOH . C 3 HOH A 114 614 133 HOH HOH . C 3 HOH A 115 615 38 HOH HOH . C 3 HOH A 116 616 110 HOH HOH . C 3 HOH A 117 617 66 HOH HOH . C 3 HOH A 118 618 115 HOH HOH . C 3 HOH A 119 619 116 HOH HOH . C 3 HOH A 120 620 43 HOH HOH . C 3 HOH A 121 621 53 HOH HOH . C 3 HOH A 122 622 112 HOH HOH . C 3 HOH A 123 623 30 HOH HOH . C 3 HOH A 124 624 32 HOH HOH . C 3 HOH A 125 625 33 HOH HOH . C 3 HOH A 126 626 48 HOH HOH . C 3 HOH A 127 627 71 HOH HOH . C 3 HOH A 128 628 80 HOH HOH . C 3 HOH A 129 629 51 HOH HOH . C 3 HOH A 130 630 46 HOH HOH . C 3 HOH A 131 631 52 HOH HOH . C 3 HOH A 132 632 117 HOH HOH . C 3 HOH A 133 633 81 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 N15 KDJ . . . B 2 17.436 2.704 13.143 1 24.91 ? N15 KDJ 401 A 1 HETATM 2 C C3 KDJ . . . B 2 16.8 6.138 14.622 1 20.68 ? C3 KDJ 401 A 1 HETATM 3 C C4 KDJ . . . B 2 16.584 4.947 13.703 1 21.81 ? C4 KDJ 401 A 1 HETATM 4 C C5 KDJ . . . B 2 17.575 3.849 14.054 1 23.29 ? C5 KDJ 401 A 1 HETATM 5 C C6 KDJ . . . B 2 17.369 3.422 15.5 1 23.66 ? C6 KDJ 401 A 1 HETATM 6 C C1 KDJ . . . B 2 17.575 4.616 16.419 1 21.53 ? C1 KDJ 401 A 1 HETATM 7 C C2 KDJ . . . B 2 16.58 5.708 16.063 1 20.06 ? C2 KDJ 401 A 1 HETATM 8 O O75 KDJ . . . B 2 17.131 2.156 9.956 1 37.55 ? O75 KDJ 401 A 1 HETATM 9 P PB5 KDJ . . . B 2 18.603 1.581 9.955 1 43.5 ? PB5 KDJ 401 A 1 HETATM 10 O O85 KDJ . . . B 2 19.747 2.649 9.738 1 43.7 ? O85 KDJ 401 A 1 HETATM 11 O O95 KDJ . . . B 2 18.787 0.285 9.222 1 49.53 ? O95 KDJ 401 A 1 HETATM 12 C C45 KDJ . . . B 2 18.846 1.08 11.735 1 37.14 ? C45 KDJ 401 A 1 HETATM 13 F F55 KDJ . . . B 2 20.039 0.514 11.877 1 39.8 ? F55 KDJ 401 A 1 HETATM 14 F F65 KDJ . . . B 2 17.901 0.213 12.084 1 35.64 ? F65 KDJ 401 A 1 HETATM 15 C C25 KDJ . . . B 2 18.759 2.318 12.63 1 31.63 ? C25 KDJ 401 A 1 HETATM 16 O O35 KDJ . . . B 2 19.779 3.045 12.839 1 31.1 ? O35 KDJ 401 A 1 HETATM 17 O O14 KDJ . . . B 2 16.777 5.352 12.34 1 25.37 ? O14 KDJ 401 A 1 HETATM 18 P PA4 KDJ . . . B 2 15.597 5.194 11.293 1 25.15 ? PA4 KDJ 401 A 1 HETATM 19 O O34 KDJ . . . B 2 16.292 4.587 10.024 1 29.47 ? O34 KDJ 401 A 1 HETATM 20 O O44 KDJ . . . B 2 15.053 6.572 11.151 1 25.37 ? O44 KDJ 401 A 1 HETATM 21 O O24 KDJ . . . B 2 14.646 4.192 12.059 1 22.82 ? O24 KDJ 401 A 1 HETATM 22 O O13 KDJ . . . B 2 15.873 7.181 14.285 1 24.01 ? O13 KDJ 401 A 1 HETATM 23 P PA3 KDJ . . . B 2 16.402 8.634 13.938 1 24.88 ? PA3 KDJ 401 A 1 HETATM 24 O O33 KDJ . . . B 2 17.023 8.483 12.505 1 31.73 ? O33 KDJ 401 A 1 HETATM 25 O O43 KDJ . . . B 2 17.354 8.945 15.039 1 27.26 ? O43 KDJ 401 A 1 HETATM 26 O O23 KDJ . . . B 2 15.058 9.464 13.983 1 27.84 ? O23 KDJ 401 A 1 HETATM 27 O O12 KDJ . . . B 2 15.245 5.203 16.211 1 18 ? O12 KDJ 401 A 1 HETATM 28 P PA2 KDJ . . . B 2 14.297 5.778 17.345 1 17.74 ? PA2 KDJ 401 A 1 HETATM 29 O O32 KDJ . . . B 2 15.132 6.94 17.988 1 18.1 ? O32 KDJ 401 A 1 HETATM 30 O O42 KDJ . . . B 2 14.023 4.602 18.216 1 17.26 ? O42 KDJ 401 A 1 HETATM 31 O O22 KDJ . . . B 2 13.06 6.258 16.488 1 17.64 ? O22 KDJ 401 A 1 HETATM 32 O O11 KDJ . . . B 2 17.376 4.213 17.782 1 23.28 ? O11 KDJ 401 A 1 HETATM 33 P PA1 KDJ . . . B 2 18.373 4.705 18.911 1 30.35 ? PA1 KDJ 401 A 1 HETATM 34 O O31 KDJ . . . B 2 19.783 4.235 18.406 1 29.66 ? O31 KDJ 401 A 1 HETATM 35 O O41 KDJ . . . B 2 18.152 6.176 18.973 1 32.06 ? O41 KDJ 401 A 1 HETATM 36 O O21 KDJ . . . B 2 17.828 3.909 20.161 1 27.82 ? O21 KDJ 401 A 1 HETATM 37 O O16 KDJ . . . B 2 18.307 2.389 15.835 1 23.46 ? O16 KDJ 401 A 1 HETATM 38 P PA6 KDJ . . . B 2 17.785 0.961 16.28 1 27.64 ? PA6 KDJ 401 A 1 HETATM 39 O O36 KDJ . . . B 2 19.091 0.179 16.66 1 30.4 ? O36 KDJ 401 A 1 HETATM 40 O O46 KDJ . . . B 2 17.04 0.463 15.092 1 25.78 ? O46 KDJ 401 A 1 HETATM 41 O O26 KDJ . . . B 2 16.871 1.343 17.511 1 27.34 ? O26 KDJ 401 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 7 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 254 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 41 #