data_5HC8 # _model_server_result.job_id vLJaUR-6IduWjj5ZlNVsyg _model_server_result.datetime_utc '2024-11-02 21:20:19' _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 5hc8 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":405}' # _entry.id 5HC8 # _exptl.entry_id 5HC8 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 262.158 _entity.id 6 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic 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 5HC8 _cell.length_a 54.211 _cell.length_b 140.235 _cell.length_c 78.702 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5HC8 _symmetry.cell_setting ? _symmetry.Int_Tables_number 20 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'C 2 2 21' # _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 _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' 3_454 -x-1,y,-z-1/2 -1 0 0 0 1 0 0 0 -1 -54.211 0 -39.351 # _struct_asym.details ? _struct_asym.entity_id 6 _struct_asym.id F _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 ASP 21 A ASP 76 1_555 B MG MG . A MG 401 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc2 B MG MG . A MG 401 1_555 C O2 PIS . A PIS 402 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.136 ? metalc ? metalc3 B MG MG . A MG 401 1_555 F O7 ISY . A ISY 405 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.12 ? metalc ? metalc4 B MG MG . A MG 401 1_555 G O HOH . A HOH 513 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.049 ? metalc ? metalc5 B MG MG . A MG 401 1_555 G O HOH . A HOH 514 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.236 ? # _chem_comp.formula 'C5 H12 O6 P2 S' _chem_comp.formula_weight 262.158 _chem_comp.id ISY _chem_comp.mon_nstd_flag . _chem_comp.name '3-methylbut-3-enylsulfanyl(phosphonooxy)phosphinic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'Isopentyl S-Thiolodiphosphate' # 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 P1 O2 ISY sing 185 n n P1 O4 ISY sing 186 n n P1 O5 ISY doub 187 n n P1 O6 ISY sing 188 n n O2 P3 ISY sing 189 n n P3 O7 ISY doub 190 n n P3 O8 ISY sing 191 n n P3 S9 ISY sing 192 n n S9 C10 ISY sing 193 n n C10 C11 ISY sing 194 n n C11 C12 ISY sing 195 n n C12 C13 ISY sing 196 n n C12 C14 ISY doub 197 n n O4 HO4 ISY sing 198 n n O6 HO6 ISY sing 199 n n O8 HO8 ISY sing 200 n n C10 H10 ISY sing 201 n n C10 H10A ISY sing 202 n n C11 H11 ISY sing 203 n n C11 H11A ISY sing 204 n n C13 H13 ISY sing 205 n n C13 H13A ISY sing 206 n n C13 H13B ISY sing 207 n n C14 H14 ISY sing 208 n n C14 H14A ISY sing 209 n n # _atom_sites.entry_id 5HC8 _atom_sites.fract_transf_matrix[1][1] 0.018446 _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] 0.007131 _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] 0.012706 _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 MG A 1 401 2 MG MG . C 3 PIS A 1 402 1 PIS DRG . D 4 61G A 1 403 1 61G ISO . E 5 SO4 A 1 404 1 SO4 SO4 . F 6 ISY A 1 405 1 ISY DSP . G 7 HOH A 1 501 47 HOH HOH . G 7 HOH A 2 502 104 HOH HOH . G 7 HOH A 3 503 97 HOH HOH . G 7 HOH A 4 504 15 HOH HOH . G 7 HOH A 5 505 49 HOH HOH . G 7 HOH A 6 506 44 HOH HOH . G 7 HOH A 7 507 45 HOH HOH . G 7 HOH A 8 508 17 HOH HOH . G 7 HOH A 9 509 52 HOH HOH . G 7 HOH A 10 510 35 HOH HOH . G 7 HOH A 11 511 20 HOH HOH . G 7 HOH A 12 512 62 HOH HOH . G 7 HOH A 13 513 1 HOH HOH . G 7 HOH A 14 514 2 HOH HOH . G 7 HOH A 15 515 38 HOH HOH . G 7 HOH A 16 516 39 HOH HOH . G 7 HOH A 17 517 3 HOH HOH . G 7 HOH A 18 518 29 HOH HOH . G 7 HOH A 19 519 108 HOH HOH . G 7 HOH A 20 520 53 HOH HOH . G 7 HOH A 21 521 124 HOH HOH . G 7 HOH A 22 522 54 HOH HOH . G 7 HOH A 23 523 23 HOH HOH . G 7 HOH A 24 524 12 HOH HOH . G 7 HOH A 25 525 129 HOH HOH . G 7 HOH A 26 526 14 HOH HOH . G 7 HOH A 27 527 26 HOH HOH . G 7 HOH A 28 528 18 HOH HOH . G 7 HOH A 29 529 119 HOH HOH . G 7 HOH A 30 530 72 HOH HOH . G 7 HOH A 31 531 78 HOH HOH . G 7 HOH A 32 532 33 HOH HOH . G 7 HOH A 33 533 4 HOH HOH . G 7 HOH A 34 534 76 HOH HOH . G 7 HOH A 35 535 28 HOH HOH . G 7 HOH A 36 536 114 HOH HOH . G 7 HOH A 37 537 50 HOH HOH . G 7 HOH A 38 538 74 HOH HOH . G 7 HOH A 39 539 51 HOH HOH . G 7 HOH A 40 540 21 HOH HOH . G 7 HOH A 41 541 120 HOH HOH . G 7 HOH A 42 542 133 HOH HOH . G 7 HOH A 43 543 13 HOH HOH . G 7 HOH A 44 544 60 HOH HOH . G 7 HOH A 45 545 34 HOH HOH . G 7 HOH A 46 546 127 HOH HOH . G 7 HOH A 47 547 16 HOH HOH . G 7 HOH A 48 548 125 HOH HOH . G 7 HOH A 49 549 86 HOH HOH . G 7 HOH A 50 550 123 HOH HOH . G 7 HOH A 51 551 65 HOH HOH . G 7 HOH A 52 552 122 HOH HOH . G 7 HOH A 53 553 5 HOH HOH . G 7 HOH A 54 554 25 HOH HOH . G 7 HOH A 55 555 27 HOH HOH . G 7 HOH A 56 556 41 HOH HOH . G 7 HOH A 57 557 22 HOH HOH . G 7 HOH A 58 558 6 HOH HOH . G 7 HOH A 59 559 135 HOH HOH . G 7 HOH A 60 560 43 HOH HOH . G 7 HOH A 61 561 24 HOH HOH . G 7 HOH A 62 562 48 HOH HOH . G 7 HOH A 63 563 8 HOH HOH . G 7 HOH A 64 564 57 HOH HOH . G 7 HOH A 65 565 130 HOH HOH . G 7 HOH A 66 566 61 HOH HOH . G 7 HOH A 67 567 46 HOH HOH . G 7 HOH A 68 568 30 HOH HOH . G 7 HOH A 69 569 31 HOH HOH . G 7 HOH A 70 570 37 HOH HOH . G 7 HOH A 71 571 88 HOH HOH . G 7 HOH A 72 572 7 HOH HOH . G 7 HOH A 73 573 32 HOH HOH . G 7 HOH A 74 574 56 HOH HOH . G 7 HOH A 75 575 9 HOH HOH . G 7 HOH A 76 576 89 HOH HOH . G 7 HOH A 77 577 105 HOH HOH . G 7 HOH A 78 578 71 HOH HOH . G 7 HOH A 79 579 19 HOH HOH . G 7 HOH A 80 580 36 HOH HOH . G 7 HOH A 81 581 11 HOH HOH . G 7 HOH A 82 582 64 HOH HOH . G 7 HOH A 83 583 40 HOH HOH . G 7 HOH A 84 584 98 HOH HOH . G 7 HOH A 85 585 59 HOH HOH . G 7 HOH A 86 586 10 HOH HOH . G 7 HOH A 87 587 58 HOH HOH . G 7 HOH A 88 588 84 HOH HOH . G 7 HOH A 89 589 115 HOH HOH . G 7 HOH A 90 590 55 HOH HOH . G 7 HOH A 91 591 75 HOH HOH . G 7 HOH A 92 592 70 HOH HOH . G 7 HOH A 93 593 69 HOH HOH . G 7 HOH A 94 594 101 HOH HOH . G 7 HOH A 95 595 42 HOH HOH . G 7 HOH A 96 596 121 HOH HOH . G 7 HOH A 97 597 80 HOH HOH . G 7 HOH A 98 598 134 HOH HOH . G 7 HOH A 99 599 106 HOH HOH . G 7 HOH A 100 600 100 HOH HOH . G 7 HOH A 101 601 95 HOH HOH . G 7 HOH A 102 602 107 HOH HOH . G 7 HOH A 103 603 111 HOH HOH . G 7 HOH A 104 604 68 HOH HOH . G 7 HOH A 105 605 109 HOH HOH . G 7 HOH A 106 606 132 HOH HOH . G 7 HOH A 107 607 112 HOH HOH . G 7 HOH A 108 608 110 HOH HOH . G 7 HOH A 109 609 83 HOH HOH . G 7 HOH A 110 610 102 HOH HOH . G 7 HOH A 111 611 113 HOH HOH . G 7 HOH A 112 612 94 HOH HOH . G 7 HOH A 113 613 99 HOH HOH . G 7 HOH A 114 614 116 HOH HOH . G 7 HOH A 115 615 87 HOH HOH . G 7 HOH A 116 616 131 HOH HOH . G 7 HOH A 117 617 128 HOH HOH . G 7 HOH A 118 618 63 HOH HOH . G 7 HOH A 119 619 137 HOH HOH . G 7 HOH A 120 621 118 HOH HOH . G 7 HOH A 121 622 93 HOH HOH . G 7 HOH A 122 623 73 HOH HOH . G 7 HOH A 123 624 66 HOH HOH . G 7 HOH A 124 625 117 HOH HOH . G 7 HOH A 125 626 92 HOH HOH . G 7 HOH A 126 627 77 HOH HOH . G 7 HOH A 127 628 96 HOH HOH . G 7 HOH A 128 629 103 HOH HOH . G 7 HOH A 129 630 79 HOH HOH . G 7 HOH A 130 631 85 HOH HOH . G 7 HOH A 131 632 81 HOH HOH . G 7 HOH A 132 633 67 HOH HOH . G 7 HOH A 133 634 91 HOH HOH . G 7 HOH A 134 635 82 HOH HOH . G 7 HOH A 135 636 126 HOH HOH . G 7 HOH A 136 637 90 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 P P1 ISY . . . F 6 -13.719 -14.195 -20.387 1 31.31 ? P1 ISY 405 A 1 HETATM 2 O O2 ISY . . . F 6 -13.281 -15.112 -19.078 1 34.67 ? O2 ISY 405 A 1 HETATM 3 P P3 ISY . . . F 6 -12.709 -14.639 -17.687 1 33.65 ? P3 ISY 405 A 1 HETATM 4 O O4 ISY . . . F 6 -14.129 -12.733 -19.952 1 36.3 ? O4 ISY 405 A 1 HETATM 5 O O5 ISY . . . F 6 -14.824 -14.855 -21.261 1 31.38 ? O5 ISY 405 A 1 HETATM 6 O O6 ISY . . . F 6 -12.453 -14.124 -21.23 1 33.52 ? O6 ISY 405 A 1 HETATM 7 O O7 ISY . . . F 6 -11.839 -13.445 -17.848 1 31.62 ? O7 ISY 405 A 1 HETATM 8 O O8 ISY . . . F 6 -12.091 -15.912 -16.944 1 33.91 ? O8 ISY 405 A 1 HETATM 9 S S9 ISY . . . F 6 -14.426 -13.932 -16.632 1 34.3 ? S9 ISY 405 A 1 HETATM 10 C C10 ISY . . . F 6 -15.073 -15.463 -16.003 1 36.99 ? C10 ISY 405 A 1 HETATM 11 C C11 ISY . . . F 6 -14.792 -15.32 -14.529 1 40.63 ? C11 ISY 405 A 1 HETATM 12 C C12 ISY . . . F 6 -14.159 -16.427 -13.734 1 35.3 ? C12 ISY 405 A 1 HETATM 13 C C13 ISY . . . F 6 -13.935 -16.221 -12.307 1 37.95 ? C13 ISY 405 A 1 HETATM 14 C C14 ISY . . . F 6 -13.582 -17.625 -14.391 1 36.43 ? C14 ISY 405 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 308 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 14 #