data_1D7U # _model_server_result.job_id 4zpoMIBZ5VIicw1E8Wyb6g _model_server_result.datetime_utc '2024-11-14 23:16:30' _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 1d7u # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":500}' # _entry.id 1D7U # _exptl.entry_id 1D7U _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.219 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '[5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate' _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 1D7U _cell.length_a 153.23 _cell.length_b 153.23 _cell.length_c 86.48 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1D7U _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3,4 # 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_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 76.615 132.701073 0 3 'crystal symmetry operation' 7_555 y,x,-z+1/3 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 28.826667 4 'crystal symmetry operation' 10_665 -y+1,-x+1,-z+1/3 0.5 -0.866025 0 -0.866025 -0.5 0 0 0 -1 76.615 132.701073 28.826667 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 O LEU 78 A LEU 78 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.662 ? metalc ? metalc2 A OG SER 80 A SER 80 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.634 ? metalc ? metalc3 A O ALA 95 A ALA 95 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.426 ? metalc ? metalc4 A O THR 98 A THR 98 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.603 ? metalc ? metalc5 A OG1 THR 98 A THR 98 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.918 ? metalc ? metalc6 A O PRO 99 A PRO 99 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.46 ? metalc ? metalc7 A O LEU 102 A LEU 102 1_555 B NA NA . A NA 435 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.666 ? metalc ? metalc8 A O THR 303 A THR 303 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.939 ? metalc ? metalc9 A O VAL 305 A VAL 305 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.813 ? metalc ? metalc10 A OD1 ASP 307 A ASP 307 1_555 C K K . A K 436 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.545 ? metalc ? metalc11 C K K . A K 436 1_555 E O HOH . A HOH 529 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.808 ? # _chem_comp.formula 'C11 H14 N3 O7 P' _chem_comp.formula_weight 331.219 _chem_comp.id LCS _chem_comp.mon_nstd_flag . _chem_comp.name '[5-hydroxy-6-methyl-4-({[(4E)-3-oxo-1,2-oxazolidin-4-ylidene]amino}methyl)pyridin-3-yl]methyl dihydrogen phosphate' _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 LCS doub 173 n y N1 C6 LCS sing 174 n y C2 C2A LCS sing 175 n n C2 C3 LCS sing 176 n y C3 O3 LCS sing 177 n n C3 C4 LCS doub 178 n y C4 C4A LCS sing 179 n n C4 C5 LCS sing 180 n y C4A N LCS sing 181 n n C5 C6 LCS doub 182 n y C5 C5A LCS sing 183 n n C5A O4P LCS sing 184 n n O4P P LCS sing 185 n n P O1P LCS doub 186 n n P O2P LCS sing 187 n n P O3P LCS sing 188 n n N CA LCS doub 189 n n CA C LCS sing 190 n n CA CB LCS sing 191 n n C O LCS doub 192 n n C ND LCS sing 193 n n ND OG LCS sing 194 n n OG CB LCS sing 195 n n C2A H2A1 LCS sing 196 n n C2A H2A2 LCS sing 197 n n C2A H2A3 LCS sing 198 n n O3 HO3 LCS sing 199 n n C4A H4A1 LCS sing 200 n n C4A H4A2 LCS sing 201 n n C6 H6 LCS sing 202 n n C5A H5A1 LCS sing 203 n n C5A H5A2 LCS sing 204 n n O2P HOP2 LCS sing 205 n n O3P HOP3 LCS sing 206 n n ND HND LCS sing 207 n n CB HB1 LCS sing 208 n n CB HB2 LCS sing 209 n n # _atom_sites.entry_id 1D7U _atom_sites.fract_transf_matrix[1][1] 0.006526 _atom_sites.fract_transf_matrix[1][2] 0.003768 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.007536 _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] 0.011563 _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 NA A 1 435 435 NA NA+ . C 3 K A 1 436 436 K K+ . D 4 LCS A 1 500 500 LCS LCS . E 5 HOH A 1 501 501 HOH WAT . E 5 HOH A 2 502 502 HOH WAT . E 5 HOH A 3 503 503 HOH WAT . E 5 HOH A 4 504 504 HOH WAT . E 5 HOH A 5 505 505 HOH WAT . E 5 HOH A 6 506 506 HOH WAT . E 5 HOH A 7 507 507 HOH WAT . E 5 HOH A 8 508 508 HOH WAT . E 5 HOH A 9 509 509 HOH WAT . E 5 HOH A 10 510 510 HOH WAT . E 5 HOH A 11 511 511 HOH WAT . E 5 HOH A 12 512 512 HOH WAT . E 5 HOH A 13 513 513 HOH WAT . E 5 HOH A 14 514 514 HOH WAT . E 5 HOH A 15 515 515 HOH WAT . E 5 HOH A 16 516 516 HOH WAT . E 5 HOH A 17 517 517 HOH WAT . E 5 HOH A 18 518 518 HOH WAT . E 5 HOH A 19 519 519 HOH WAT . E 5 HOH A 20 520 520 HOH WAT . E 5 HOH A 21 521 521 HOH WAT . E 5 HOH A 22 522 522 HOH WAT . E 5 HOH A 23 523 523 HOH WAT . E 5 HOH A 24 524 524 HOH WAT . E 5 HOH A 25 525 525 HOH WAT . E 5 HOH A 26 526 526 HOH WAT . E 5 HOH A 27 527 527 HOH WAT . E 5 HOH A 28 528 528 HOH WAT . E 5 HOH A 29 529 529 HOH WAT . E 5 HOH A 30 530 530 HOH WAT . E 5 HOH A 31 531 531 HOH WAT . E 5 HOH A 32 532 532 HOH WAT . E 5 HOH A 33 533 533 HOH WAT . E 5 HOH A 34 534 534 HOH WAT . E 5 HOH A 35 535 535 HOH WAT . E 5 HOH A 36 536 536 HOH WAT . E 5 HOH A 37 537 537 HOH WAT . E 5 HOH A 38 538 538 HOH WAT . E 5 HOH A 39 539 539 HOH WAT . E 5 HOH A 40 540 540 HOH WAT . E 5 HOH A 41 541 541 HOH WAT . E 5 HOH A 42 542 542 HOH WAT . E 5 HOH A 43 543 543 HOH WAT . E 5 HOH A 44 544 544 HOH WAT . E 5 HOH A 45 545 545 HOH WAT . E 5 HOH A 46 546 546 HOH WAT . E 5 HOH A 47 547 547 HOH WAT . E 5 HOH A 48 548 548 HOH WAT . E 5 HOH A 49 549 549 HOH WAT . E 5 HOH A 50 550 550 HOH WAT . E 5 HOH A 51 551 551 HOH WAT . E 5 HOH A 52 552 552 HOH WAT . E 5 HOH A 53 553 553 HOH WAT . E 5 HOH A 54 554 554 HOH WAT . E 5 HOH A 55 555 555 HOH WAT . E 5 HOH A 56 556 556 HOH WAT . E 5 HOH A 57 557 557 HOH WAT . E 5 HOH A 58 558 558 HOH WAT . E 5 HOH A 59 559 559 HOH WAT . E 5 HOH A 60 560 560 HOH WAT . E 5 HOH A 61 561 561 HOH WAT . E 5 HOH A 62 562 562 HOH WAT . E 5 HOH A 63 563 563 HOH WAT . E 5 HOH A 64 564 564 HOH WAT . E 5 HOH A 65 565 565 HOH WAT . E 5 HOH A 66 566 566 HOH WAT . E 5 HOH A 67 568 568 HOH WAT . E 5 HOH A 68 569 569 HOH WAT . E 5 HOH A 69 570 570 HOH WAT . E 5 HOH A 70 571 571 HOH WAT . E 5 HOH A 71 573 573 HOH WAT . E 5 HOH A 72 574 574 HOH WAT . E 5 HOH A 73 575 575 HOH WAT . E 5 HOH A 74 576 576 HOH WAT . E 5 HOH A 75 577 577 HOH WAT . E 5 HOH A 76 578 578 HOH WAT . E 5 HOH A 77 579 579 HOH WAT . E 5 HOH A 78 580 580 HOH WAT . E 5 HOH A 79 581 581 HOH WAT . E 5 HOH A 80 582 582 HOH WAT . E 5 HOH A 81 583 583 HOH WAT . E 5 HOH A 82 584 584 HOH WAT . E 5 HOH A 83 585 585 HOH WAT . E 5 HOH A 84 586 586 HOH WAT . E 5 HOH A 85 587 587 HOH WAT . E 5 HOH A 86 588 588 HOH WAT . E 5 HOH A 87 590 590 HOH WAT . E 5 HOH A 88 601 601 HOH WAT . E 5 HOH A 89 602 602 HOH WAT . E 5 HOH A 90 603 603 HOH WAT . E 5 HOH A 91 604 604 HOH WAT . E 5 HOH A 92 605 605 HOH WAT . E 5 HOH A 93 606 606 HOH WAT . E 5 HOH A 94 607 607 HOH WAT . E 5 HOH A 95 608 608 HOH WAT . E 5 HOH A 96 609 609 HOH WAT . E 5 HOH A 97 610 610 HOH WAT . E 5 HOH A 98 611 611 HOH WAT . E 5 HOH A 99 612 612 HOH WAT . E 5 HOH A 100 613 613 HOH WAT . E 5 HOH A 101 614 614 HOH WAT . E 5 HOH A 102 615 615 HOH WAT . E 5 HOH A 103 616 616 HOH WAT . E 5 HOH A 104 617 617 HOH WAT . E 5 HOH A 105 618 618 HOH WAT . E 5 HOH A 106 619 619 HOH WAT . E 5 HOH A 107 621 621 HOH WAT . E 5 HOH A 108 622 622 HOH WAT . E 5 HOH A 109 624 624 HOH WAT . E 5 HOH A 110 625 625 HOH WAT . E 5 HOH A 111 627 627 HOH WAT . E 5 HOH A 112 629 629 HOH WAT . E 5 HOH A 113 630 630 HOH WAT . E 5 HOH A 114 631 631 HOH WAT . E 5 HOH A 115 632 632 HOH WAT . E 5 HOH A 116 633 633 HOH WAT . E 5 HOH A 117 635 635 HOH WAT . E 5 HOH A 118 636 636 HOH WAT . E 5 HOH A 119 638 638 HOH WAT . E 5 HOH A 120 639 639 HOH WAT . E 5 HOH A 121 641 641 HOH WAT . E 5 HOH A 122 642 642 HOH WAT . E 5 HOH A 123 643 643 HOH WAT . E 5 HOH A 124 645 645 HOH WAT . E 5 HOH A 125 647 647 HOH WAT . E 5 HOH A 126 648 648 HOH WAT . E 5 HOH A 127 649 649 HOH WAT . E 5 HOH A 128 650 650 HOH WAT . E 5 HOH A 129 651 651 HOH WAT . E 5 HOH A 130 652 652 HOH WAT . E 5 HOH A 131 653 653 HOH WAT . E 5 HOH A 132 654 654 HOH WAT . E 5 HOH A 133 655 655 HOH WAT . E 5 HOH A 134 656 656 HOH WAT . E 5 HOH A 135 657 657 HOH WAT . E 5 HOH A 136 658 658 HOH WAT . E 5 HOH A 137 660 660 HOH WAT . E 5 HOH A 138 661 661 HOH WAT . E 5 HOH A 139 662 662 HOH WAT . E 5 HOH A 140 665 665 HOH WAT . E 5 HOH A 141 668 668 HOH WAT . E 5 HOH A 142 669 669 HOH WAT . E 5 HOH A 143 670 670 HOH WAT . E 5 HOH A 144 671 671 HOH WAT . E 5 HOH A 145 672 672 HOH WAT . E 5 HOH A 146 673 673 HOH WAT . E 5 HOH A 147 674 674 HOH WAT . E 5 HOH A 148 675 675 HOH WAT . # 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 LCS . . . D 4 17.548 53.571 13.857 1 30.39 ? N1 LCS 500 A 1 HETATM 2 C C2 LCS . . . D 4 16.476 53.854 14.628 1 41.88 ? C2 LCS 500 A 1 HETATM 3 C C2A LCS . . . D 4 15.458 54.823 14.09 1 34.46 ? C2A LCS 500 A 1 HETATM 4 C C3 LCS . . . D 4 16.37 53.23 15.9 1 36.21 ? C3 LCS 500 A 1 HETATM 5 O O3 LCS . . . D 4 15.254 53.532 16.639 1 29.66 ? O3 LCS 500 A 1 HETATM 6 C C4 LCS . . . D 4 17.382 52.396 16.321 1 31.89 ? C4 LCS 500 A 1 HETATM 7 C C4A LCS . . . D 4 17.314 51.669 17.547 1 61.68 ? C4A LCS 500 A 1 HETATM 8 C C5 LCS . . . D 4 18.441 52.118 15.409 1 31.28 ? C5 LCS 500 A 1 HETATM 9 C C6 LCS . . . D 4 18.532 52.73 14.203 1 29.96 ? C6 LCS 500 A 1 HETATM 10 C C5A LCS . . . D 4 19.623 51.216 15.864 1 28.58 ? C5A LCS 500 A 1 HETATM 11 O O4P LCS . . . D 4 19.367 49.83 15.843 1 37.9 ? O4P LCS 500 A 1 HETATM 12 P P LCS . . . D 4 20.32 48.839 16.721 1 31.61 ? P LCS 500 A 1 HETATM 13 O O1P LCS . . . D 4 20.248 49.289 18.125 1 37.52 ? O1P LCS 500 A 1 HETATM 14 O O2P LCS . . . D 4 19.767 47.392 16.569 1 35.93 ? O2P LCS 500 A 1 HETATM 15 O O3P LCS . . . D 4 21.654 48.881 16.081 1 26.8 ? O3P LCS 500 A 1 HETATM 16 N N LCS . . . D 4 16.361 51.939 18.337 1 50.38 ? N LCS 500 A 1 HETATM 17 C CA LCS . . . D 4 16.429 51.685 19.632 1 100 ? CA LCS 500 A 1 HETATM 18 C C LCS . . . D 4 15.488 52.01 20.583 1 98.68 ? C LCS 500 A 1 HETATM 19 O O LCS . . . D 4 14.325 52.585 20.621 1 40.92 ? O LCS 500 A 1 HETATM 20 N ND LCS . . . D 4 15.942 51.592 21.726 1 42.43 ? ND LCS 500 A 1 HETATM 21 O OG LCS . . . D 4 17.191 50.934 21.514 1 83 ? OG LCS 500 A 1 HETATM 22 C CB LCS . . . D 4 17.516 51.017 20.189 1 100 ? CB LCS 500 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 221 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 22 #