data_4D9E # _model_server_result.job_id TTbLGWztJ7gCyPc0s3u4Nw _model_server_result.datetime_utc '2025-06-20 12:56:04' _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 4d9e # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"H","auth_seq_id":402}' # _entry.id 4D9E # _exptl.entry_id 4D9E _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 331.219 _entity.id 3 _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 4 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 90 _cell.angle_beta 119.03 _cell.angle_gamma 90 _cell.entry_id 4D9E _cell.length_a 66.42 _cell.length_b 165.84 _cell.length_c 68.06 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4D9E _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA dimeric 2 author_and_software_defined_assembly 1 PISA dimeric 2 author_and_software_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,E,F,G,H,L,M 1 1 C,D,I,J,K,N,O 2 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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 3 F N N ? 3 H N N ? 3 I N N ? 3 K N N # _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 190 n y N1 C6 LCS sing 191 n y C2 C2A LCS sing 192 n n C2 C3 LCS sing 193 n y C3 O3 LCS sing 194 n n C3 C4 LCS doub 195 n y C4 C4A LCS sing 196 n n C4 C5 LCS sing 197 n y C4A N LCS sing 198 n n C5 C6 LCS doub 199 n y C5 C5A LCS sing 200 n n C5A O4P LCS sing 201 n n O4P P LCS sing 202 n n P O1P LCS doub 203 n n P O2P LCS sing 204 n n P O3P LCS sing 205 n n N CA LCS doub 206 n n CA C LCS sing 207 n n CA CB LCS sing 208 n n C O LCS doub 209 n n C ND LCS sing 210 n n ND OG LCS sing 211 n n OG CB LCS sing 212 n n C2A H2A1 LCS sing 213 n n C2A H2A2 LCS sing 214 n n C2A H2A3 LCS sing 215 n n O3 HO3 LCS sing 216 n n C4A H4A1 LCS sing 217 n n C4A H4A2 LCS sing 218 n n C6 H6 LCS sing 219 n n C5A H5A1 LCS sing 220 n n C5A H5A2 LCS sing 221 n n O2P HOP2 LCS sing 222 n n O3P HOP3 LCS sing 223 n n ND HND LCS sing 224 n n CB HB1 LCS sing 225 n n CB HB2 LCS sing 226 n n # _atom_sites.entry_id 4D9E _atom_sites.fract_transf_matrix[1][1] 0.015056 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.008356 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00603 _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] 0.016804 _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 E 2 BEN A 1 401 402 BEN BEN . F 3 LCS A 1 402 1 LCS LCS . G 2 BEN B 1 401 1 BEN BEN . H 3 LCS B 1 402 1 LCS LCS . I 3 LCS C 1 401 1 LCS LCS . J 2 BEN D 1 401 403 BEN BEN . K 3 LCS D 1 402 1 LCS LCS . L 4 HOH A 1 501 1 HOH HOH . L 4 HOH A 2 502 3 HOH HOH . L 4 HOH A 3 503 8 HOH HOH . L 4 HOH A 4 504 9 HOH HOH . L 4 HOH A 5 505 12 HOH HOH . L 4 HOH A 6 506 13 HOH HOH . L 4 HOH A 7 507 16 HOH HOH . L 4 HOH A 8 508 18 HOH HOH . L 4 HOH A 9 509 22 HOH HOH . L 4 HOH A 10 510 24 HOH HOH . L 4 HOH A 11 511 32 HOH HOH . L 4 HOH A 12 512 35 HOH HOH . L 4 HOH A 13 513 46 HOH HOH . L 4 HOH A 14 514 47 HOH HOH . L 4 HOH A 15 515 52 HOH HOH . L 4 HOH A 16 516 56 HOH HOH . L 4 HOH A 17 517 58 HOH HOH . L 4 HOH A 18 518 60 HOH HOH . L 4 HOH A 19 519 61 HOH HOH . L 4 HOH A 20 520 62 HOH HOH . L 4 HOH A 21 521 65 HOH HOH . L 4 HOH A 22 522 75 HOH HOH . L 4 HOH A 23 523 78 HOH HOH . L 4 HOH A 24 524 79 HOH HOH . L 4 HOH A 25 525 82 HOH HOH . L 4 HOH A 26 526 83 HOH HOH . L 4 HOH A 27 527 86 HOH HOH . L 4 HOH A 28 528 90 HOH HOH . L 4 HOH A 29 529 92 HOH HOH . L 4 HOH A 30 530 94 HOH HOH . L 4 HOH A 31 531 95 HOH HOH . L 4 HOH A 32 532 96 HOH HOH . L 4 HOH A 33 533 99 HOH HOH . L 4 HOH A 34 534 104 HOH HOH . L 4 HOH A 35 535 107 HOH HOH . L 4 HOH A 36 536 111 HOH HOH . L 4 HOH A 37 537 114 HOH HOH . L 4 HOH A 38 538 124 HOH HOH . L 4 HOH A 39 539 127 HOH HOH . L 4 HOH A 40 540 128 HOH HOH . L 4 HOH A 41 541 129 HOH HOH . L 4 HOH A 42 542 133 HOH HOH . L 4 HOH A 43 543 134 HOH HOH . L 4 HOH A 44 544 136 HOH HOH . L 4 HOH A 45 545 138 HOH HOH . L 4 HOH A 46 546 140 HOH HOH . L 4 HOH A 47 547 142 HOH HOH . L 4 HOH A 48 548 144 HOH HOH . L 4 HOH A 49 549 145 HOH HOH . L 4 HOH A 50 550 158 HOH HOH . L 4 HOH A 51 551 160 HOH HOH . L 4 HOH A 52 552 161 HOH HOH . L 4 HOH A 53 553 163 HOH HOH . L 4 HOH A 54 554 166 HOH HOH . L 4 HOH A 55 555 170 HOH HOH . L 4 HOH A 56 556 171 HOH HOH . L 4 HOH A 57 557 182 HOH HOH . L 4 HOH A 58 558 184 HOH HOH . L 4 HOH A 59 559 190 HOH HOH . L 4 HOH A 60 560 191 HOH HOH . L 4 HOH A 61 561 192 HOH HOH . L 4 HOH A 62 562 196 HOH HOH . L 4 HOH A 63 563 200 HOH HOH . L 4 HOH A 64 564 208 HOH HOH . L 4 HOH A 65 565 222 HOH HOH . L 4 HOH A 66 566 232 HOH HOH . L 4 HOH A 67 567 235 HOH HOH . L 4 HOH A 68 568 3 HOH HOH . M 4 HOH B 1 501 6 HOH HOH . M 4 HOH B 2 502 7 HOH HOH . M 4 HOH B 3 503 10 HOH HOH . M 4 HOH B 4 504 17 HOH HOH . M 4 HOH B 5 505 21 HOH HOH . M 4 HOH B 6 506 25 HOH HOH . M 4 HOH B 7 507 26 HOH HOH . M 4 HOH B 8 508 36 HOH HOH . M 4 HOH B 9 509 39 HOH HOH . M 4 HOH B 10 510 43 HOH HOH . M 4 HOH B 11 511 53 HOH HOH . M 4 HOH B 12 512 55 HOH HOH . M 4 HOH B 13 513 66 HOH HOH . M 4 HOH B 14 514 73 HOH HOH . M 4 HOH B 15 515 81 HOH HOH . M 4 HOH B 16 516 87 HOH HOH . M 4 HOH B 17 517 103 HOH HOH . M 4 HOH B 18 518 109 HOH HOH . M 4 HOH B 19 519 115 HOH HOH . M 4 HOH B 20 520 116 HOH HOH . M 4 HOH B 21 521 117 HOH HOH . M 4 HOH B 22 522 118 HOH HOH . M 4 HOH B 23 523 120 HOH HOH . M 4 HOH B 24 524 130 HOH HOH . M 4 HOH B 25 525 131 HOH HOH . M 4 HOH B 26 526 146 HOH HOH . M 4 HOH B 27 527 159 HOH HOH . M 4 HOH B 28 528 162 HOH HOH . M 4 HOH B 29 529 164 HOH HOH . M 4 HOH B 30 530 167 HOH HOH . M 4 HOH B 31 531 168 HOH HOH . M 4 HOH B 32 532 172 HOH HOH . M 4 HOH B 33 533 176 HOH HOH . M 4 HOH B 34 534 179 HOH HOH . M 4 HOH B 35 535 181 HOH HOH . M 4 HOH B 36 536 185 HOH HOH . M 4 HOH B 37 537 189 HOH HOH . M 4 HOH B 38 538 195 HOH HOH . M 4 HOH B 39 539 197 HOH HOH . M 4 HOH B 40 540 198 HOH HOH . M 4 HOH B 41 541 199 HOH HOH . M 4 HOH B 42 542 202 HOH HOH . M 4 HOH B 43 543 205 HOH HOH . M 4 HOH B 44 544 206 HOH HOH . M 4 HOH B 45 545 215 HOH HOH . M 4 HOH B 46 546 218 HOH HOH . M 4 HOH B 47 547 220 HOH HOH . M 4 HOH B 48 548 221 HOH HOH . M 4 HOH B 49 549 230 HOH HOH . M 4 HOH B 50 550 231 HOH HOH . M 4 HOH B 51 551 234 HOH HOH . M 4 HOH B 52 552 239 HOH HOH . M 4 HOH B 53 553 1 HOH HOH . N 4 HOH C 1 501 4 HOH HOH . N 4 HOH C 2 502 11 HOH HOH . N 4 HOH C 3 503 14 HOH HOH . N 4 HOH C 4 504 15 HOH HOH . N 4 HOH C 5 505 19 HOH HOH . N 4 HOH C 6 506 20 HOH HOH . N 4 HOH C 7 507 23 HOH HOH . N 4 HOH C 8 508 28 HOH HOH . N 4 HOH C 9 509 30 HOH HOH . N 4 HOH C 10 510 31 HOH HOH . N 4 HOH C 11 511 33 HOH HOH . N 4 HOH C 12 512 40 HOH HOH . N 4 HOH C 13 513 57 HOH HOH . N 4 HOH C 14 514 63 HOH HOH . N 4 HOH C 15 515 72 HOH HOH . N 4 HOH C 16 516 77 HOH HOH . N 4 HOH C 17 517 80 HOH HOH . N 4 HOH C 18 518 84 HOH HOH . N 4 HOH C 19 519 89 HOH HOH . N 4 HOH C 20 520 93 HOH HOH . N 4 HOH C 21 521 105 HOH HOH . N 4 HOH C 22 522 108 HOH HOH . N 4 HOH C 23 523 121 HOH HOH . N 4 HOH C 24 524 132 HOH HOH . N 4 HOH C 25 525 135 HOH HOH . N 4 HOH C 26 526 143 HOH HOH . N 4 HOH C 27 527 147 HOH HOH . N 4 HOH C 28 528 149 HOH HOH . N 4 HOH C 29 529 151 HOH HOH . N 4 HOH C 30 530 153 HOH HOH . N 4 HOH C 31 531 156 HOH HOH . N 4 HOH C 32 532 174 HOH HOH . N 4 HOH C 33 533 175 HOH HOH . N 4 HOH C 34 534 178 HOH HOH . N 4 HOH C 35 535 187 HOH HOH . N 4 HOH C 36 536 188 HOH HOH . N 4 HOH C 37 537 193 HOH HOH . N 4 HOH C 38 538 203 HOH HOH . N 4 HOH C 39 539 204 HOH HOH . N 4 HOH C 40 540 207 HOH HOH . N 4 HOH C 41 541 212 HOH HOH . N 4 HOH C 42 542 214 HOH HOH . N 4 HOH C 43 543 219 HOH HOH . N 4 HOH C 44 544 223 HOH HOH . N 4 HOH C 45 545 225 HOH HOH . N 4 HOH C 46 546 227 HOH HOH . N 4 HOH C 47 547 228 HOH HOH . N 4 HOH C 48 548 229 HOH HOH . N 4 HOH C 49 549 238 HOH HOH . N 4 HOH C 50 550 241 HOH HOH . N 4 HOH C 51 551 1 HOH HOH . N 4 HOH C 52 552 2 HOH HOH . N 4 HOH C 53 553 4 HOH HOH . N 4 HOH C 54 554 8 HOH HOH . O 4 HOH D 1 501 2 HOH HOH . O 4 HOH D 2 502 5 HOH HOH . O 4 HOH D 3 503 27 HOH HOH . O 4 HOH D 4 504 29 HOH HOH . O 4 HOH D 5 505 34 HOH HOH . O 4 HOH D 6 506 38 HOH HOH . O 4 HOH D 7 507 41 HOH HOH . O 4 HOH D 8 508 42 HOH HOH . O 4 HOH D 9 509 44 HOH HOH . O 4 HOH D 10 510 45 HOH HOH . O 4 HOH D 11 511 48 HOH HOH . O 4 HOH D 12 512 49 HOH HOH . O 4 HOH D 13 513 50 HOH HOH . O 4 HOH D 14 514 51 HOH HOH . O 4 HOH D 15 515 54 HOH HOH . O 4 HOH D 16 516 59 HOH HOH . O 4 HOH D 17 517 64 HOH HOH . O 4 HOH D 18 518 67 HOH HOH . O 4 HOH D 19 519 69 HOH HOH . O 4 HOH D 20 520 70 HOH HOH . O 4 HOH D 21 521 71 HOH HOH . O 4 HOH D 22 522 74 HOH HOH . O 4 HOH D 23 523 76 HOH HOH . O 4 HOH D 24 524 85 HOH HOH . O 4 HOH D 25 525 88 HOH HOH . O 4 HOH D 26 526 91 HOH HOH . O 4 HOH D 27 527 97 HOH HOH . O 4 HOH D 28 528 98 HOH HOH . O 4 HOH D 29 529 100 HOH HOH . O 4 HOH D 30 530 101 HOH HOH . O 4 HOH D 31 531 102 HOH HOH . O 4 HOH D 32 532 106 HOH HOH . O 4 HOH D 33 533 110 HOH HOH . O 4 HOH D 34 534 112 HOH HOH . O 4 HOH D 35 535 113 HOH HOH . O 4 HOH D 36 536 119 HOH HOH . O 4 HOH D 37 537 122 HOH HOH . O 4 HOH D 38 538 123 HOH HOH . O 4 HOH D 39 539 125 HOH HOH . O 4 HOH D 40 540 126 HOH HOH . O 4 HOH D 41 541 137 HOH HOH . O 4 HOH D 42 542 139 HOH HOH . O 4 HOH D 43 543 141 HOH HOH . O 4 HOH D 44 544 148 HOH HOH . O 4 HOH D 45 545 150 HOH HOH . O 4 HOH D 46 546 152 HOH HOH . O 4 HOH D 47 547 154 HOH HOH . O 4 HOH D 48 548 155 HOH HOH . O 4 HOH D 49 549 157 HOH HOH . O 4 HOH D 50 550 165 HOH HOH . O 4 HOH D 51 551 169 HOH HOH . O 4 HOH D 52 552 173 HOH HOH . O 4 HOH D 53 553 177 HOH HOH . O 4 HOH D 54 554 180 HOH HOH . O 4 HOH D 55 555 183 HOH HOH . O 4 HOH D 56 556 194 HOH HOH . O 4 HOH D 57 557 201 HOH HOH . O 4 HOH D 58 558 209 HOH HOH . O 4 HOH D 59 559 211 HOH HOH . O 4 HOH D 60 560 213 HOH HOH . O 4 HOH D 61 561 216 HOH HOH . O 4 HOH D 62 562 217 HOH HOH . O 4 HOH D 63 563 224 HOH HOH . O 4 HOH D 64 564 226 HOH HOH . O 4 HOH D 65 565 233 HOH HOH . O 4 HOH D 66 566 236 HOH HOH . O 4 HOH D 67 567 240 HOH HOH . O 4 HOH D 68 568 242 HOH HOH . O 4 HOH D 69 569 243 HOH HOH . O 4 HOH D 70 570 244 HOH HOH . O 4 HOH D 71 571 5 HOH HOH . O 4 HOH D 72 572 6 HOH HOH . O 4 HOH D 73 573 7 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 LCS . . . H 3 5.808 45.115 42.24 1 20.48 ? N1 LCS 402 B 1 HETATM 2 C C2 LCS . . . H 3 4.66 44.723 41.747 1 19.99 ? C2 LCS 402 B 1 HETATM 3 C C2A LCS . . . H 3 4.652 44.585 40.277 1 19.79 ? C2A LCS 402 B 1 HETATM 4 C C3 LCS . . . H 3 3.496 44.488 42.601 1 19.21 ? C3 LCS 402 B 1 HETATM 5 O O3 LCS . . . H 3 2.354 44.127 42.091 1 19.23 ? O3 LCS 402 B 1 HETATM 6 C C4 LCS . . . H 3 3.684 44.72 44.024 1 20.56 ? C4 LCS 402 B 1 HETATM 7 C C4A LCS . . . H 3 2.827 44.525 45.244 1 21.2 ? C4A LCS 402 B 1 HETATM 8 C C5 LCS . . . H 3 5.044 45.13 44.423 1 20.95 ? C5 LCS 402 B 1 HETATM 9 C C6 LCS . . . H 3 6.02 45.311 43.494 1 20.76 ? C6 LCS 402 B 1 HETATM 10 C C5A LCS . . . H 3 5.356 45.378 45.858 1 20.95 ? C5A LCS 402 B 1 HETATM 11 O O4P LCS . . . H 3 5.847 44.251 46.502 1 21.59 ? O4P LCS 402 B 1 HETATM 12 P P LCS . . . H 3 5.867 44.127 48.049 1 24.13 ? P LCS 402 B 1 HETATM 13 O O1P LCS . . . H 3 4.558 44.548 48.332 1 21.49 ? O1P LCS 402 B 1 HETATM 14 O O2P LCS . . . H 3 6.961 45.003 48.313 1 21.9 ? O2P LCS 402 B 1 HETATM 15 O O3P LCS . . . H 3 6.101 42.741 48.241 1 20.34 ? O3P LCS 402 B 1 HETATM 16 N N LCS . . . H 3 1.452 44.602 45.487 1 21.56 ? N LCS 402 B 1 HETATM 17 C CA LCS . . . H 3 1.057 45.177 46.764 0.5 21.33 ? CA LCS 402 B 1 HETATM 18 C C LCS . . . H 3 -0.274 45.852 46.761 0.5 21.71 ? C LCS 402 B 1 HETATM 19 O O LCS . . . H 3 -1.273 45.364 46.24 0.5 22.09 ? O LCS 402 B 1 HETATM 20 N ND LCS . . . H 3 -0.206 47.031 47.356 0.5 21.74 ? ND LCS 402 B 1 HETATM 21 O OG LCS . . . H 3 1.035 47.429 47.389 0.5 21.93 ? OG LCS 402 B 1 HETATM 22 C CB LCS . . . H 3 1.929 46.366 47.131 0.5 21.41 ? CB LCS 402 B 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 11 _model_server_stats.query_time_ms 288 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 22 #