data_9MNN # _model_server_result.job_id ebgkU0ciWAahEYhn5EdNag _model_server_result.datetime_utc '2025-08-05 00:25:51' _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 9mnn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":601}' # _entry.id 9MNN # _exptl.entry_id 9MNN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 527.403 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic 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 120 _cell.entry_id 9MNN _cell.length_a 175.226 _cell.length_b 175.226 _cell.length_c 100.228 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 9MNN _symmetry.cell_setting ? _symmetry.Int_Tables_number 181 _symmetry.space_group_name_Hall 'P 64 2 (x,y,z+1/6)' _symmetry.space_group_name_H-M 'P 64 2 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _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 _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_545 -x,-y-1,z -1 0 0 0 -1 0 0 0 1 87.613 -151.750167 0 3 'crystal symmetry operation' 9_554 -x,-x+y,-z-1/3 -0.5 -0.866025 0 -0.866025 0.5 0 0 0 -1 0 0 -33.409333 4 'crystal symmetry operation' 12_544 x,x-y-1,-z-1/3 0.5 0.866025 0 0.866025 -0.5 0 0 0 -1 87.613 -151.750167 -33.409333 # _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 # 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 ALA 46 A ALA 43 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.541 ? metalc ? metalc2 A O HIS 48 A HIS 45 1_555 D MG MG . A MG 603 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.989 ? metalc ? metalc3 A OD1 ASP 462 A ASP 459 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.825 ? metalc ? metalc4 A OD1 ASN 489 A ASN 486 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.202 ? metalc ? metalc5 A O GLY 491 A GLY 488 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.755 ? metalc ? metalc6 B O2A TD6 . A TD6 601 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.206 ? metalc ? metalc7 B O2B TD6 . A TD6 601 1_555 C MG MG . A MG 602 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc8 D MG MG . A MG 603 1_555 E O HOH . A HOH 702 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.267 ? metalc ? metalc9 D MG MG . A MG 603 1_555 E O HOH . A HOH 717 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc10 D MG MG . A MG 603 1_555 E O HOH . A HOH 719 4_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.119 ? metalc ? metalc11 D MG MG . A MG 603 1_555 E O HOH . A HOH 726 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.468 ? # _chem_comp.formula 'C16 H25 N4 O10 P2 S 1' _chem_comp.formula_weight 527.403 _chem_comp.id TD6 _chem_comp.mon_nstd_flag . _chem_comp.name '(4S)-4-{3-[(4-amino-2-methylpyrimidin-5-yl)methyl]-5-(2-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}ethyl)-4-methyl-1,3lambda~5~-thiazol-2-yl}-4-hydroxybutanoic 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 C2 S1 TD6 sing 290 n y S1 C5 TD6 sing 291 n y C11 C2 TD6 sing 292 n n C2 N3 TD6 doub 293 n y C7' N3 TD6 sing 294 n n N3 C4 TD6 sing 295 n y C4 C5 TD6 doub 296 n y C4 CM4 TD6 sing 297 n n C5 C6 TD6 sing 298 n n C6 C7 TD6 sing 299 n n C6 H6 TD6 sing 300 n n C6 H6A TD6 sing 301 n n C7 O7 TD6 sing 302 n n C7 H7 TD6 sing 303 n n C7 H7A TD6 sing 304 n n O7 PA TD6 sing 305 n n O3A PA TD6 sing 306 n n O1A PA TD6 doub 307 n n PA O2A TD6 sing 308 n n O2B PB TD6 doub 309 n n O3B PB TD6 sing 310 n n PB O3A TD6 sing 311 n n PB O1B TD6 sing 312 n n C2' N1' TD6 doub 313 n y N1' C6' TD6 sing 314 n y OL1 C11 TD6 sing 315 n n C11 CLB TD6 sing 316 n n C11 H11 TD6 sing 317 n n CLB C13 TD6 sing 318 n n CLC C13 TD6 sing 319 n n C13 H13 TD6 sing 320 n n C13 H13A TD6 sing 321 n n O1B HO1B TD6 sing 322 n n N3' C2' TD6 sing 323 n y CM2 C2' TD6 sing 324 n n O2A HO2A TD6 sing 325 n n N3' C4' TD6 doub 326 n y O3B HO3B TD6 sing 327 n n N4' C4' TD6 sing 328 n n C4' C5' TD6 sing 329 n y N4' HN4' TD6 sing 330 n n N4' HN4A TD6 sing 331 n n C5' C7' TD6 sing 332 n n C5' C6' TD6 doub 333 n y C6' H6' TD6 sing 334 n n C7' H7' TD6 sing 335 n n C7' "H7'A" TD6 sing 336 n n OL1 HOL1 TD6 sing 337 n n CLC OL2 TD6 sing 338 n n OL2 HOL2 TD6 sing 339 n n OL3 CLC TD6 doub 340 n n CLB HLB TD6 sing 341 n n CLB HLBA TD6 sing 342 n n CM2 HM2 TD6 sing 343 n n CM2 HM2A TD6 sing 344 n n CM2 HM2B TD6 sing 345 n n CM4 HM4 TD6 sing 346 n n CM4 HM4A TD6 sing 347 n n CM4 HM4B TD6 sing 348 n n # _atom_sites.entry_id 9MNN _atom_sites.fract_transf_matrix[1][1] 0.005707 _atom_sites.fract_transf_matrix[1][2] 0.003295 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.00659 _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] 0.009977 _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 TD6 A 1 601 601 TD6 TD6 . C 3 MG A 1 602 1 MG MG . D 3 MG A 1 603 2 MG MG . E 4 HOH A 1 701 27 HOH HOH . E 4 HOH A 2 702 21 HOH HOH . E 4 HOH A 3 703 1 HOH HOH . E 4 HOH A 4 704 11 HOH HOH . E 4 HOH A 5 705 6 HOH HOH . E 4 HOH A 6 706 2 HOH HOH . E 4 HOH A 7 707 14 HOH HOH . E 4 HOH A 8 708 5 HOH HOH . E 4 HOH A 9 709 15 HOH HOH . E 4 HOH A 10 710 13 HOH HOH . E 4 HOH A 11 711 17 HOH HOH . E 4 HOH A 12 712 16 HOH HOH . E 4 HOH A 13 713 23 HOH HOH . E 4 HOH A 14 714 25 HOH HOH . E 4 HOH A 15 715 12 HOH HOH . E 4 HOH A 16 716 3 HOH HOH . E 4 HOH A 17 717 19 HOH HOH . E 4 HOH A 18 718 9 HOH HOH . E 4 HOH A 19 719 20 HOH HOH . E 4 HOH A 20 720 22 HOH HOH . E 4 HOH A 21 721 10 HOH HOH . E 4 HOH A 22 722 7 HOH HOH . E 4 HOH A 23 723 4 HOH HOH . E 4 HOH A 24 724 24 HOH HOH . E 4 HOH A 25 725 26 HOH HOH . E 4 HOH A 26 726 18 HOH HOH . E 4 HOH A 27 727 8 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 S S1 TD6 . . . B 2 41.5 -59.398 8.512 1 61.96 ? S1 TD6 601 A 1 HETATM 2 C C2 TD6 . . . B 2 41.224 -59.881 6.931 1 84.84 ? C2 TD6 601 A 1 HETATM 3 N N3 TD6 . . . B 2 40.378 -60.963 6.907 1 78.81 ? N3 TD6 601 A 1 HETATM 4 C C4 TD6 . . . B 2 39.98 -61.351 8.209 1 72.97 ? C4 TD6 601 A 1 HETATM 5 C C5 TD6 . . . B 2 40.528 -60.556 9.231 1 72 ? C5 TD6 601 A 1 HETATM 6 C C6 TD6 . . . B 2 40.385 -60.603 10.71 1 57.17 ? C6 TD6 601 A 1 HETATM 7 C C7 TD6 . . . B 2 41.727 -60.817 11.359 1 59.75 ? C7 TD6 601 A 1 HETATM 8 O O7 TD6 . . . B 2 41.586 -60.696 12.796 1 63.94 ? O7 TD6 601 A 1 HETATM 9 P PA TD6 . . . B 2 42.893 -60.718 13.733 1 49.53 ? PA TD6 601 A 1 HETATM 10 P PB TD6 . . . B 2 42.792 -57.789 14.107 1 70.51 ? PB TD6 601 A 1 HETATM 11 N N1' TD6 . . . B 2 40.524 -65.383 5.401 1 68.02 ? N1' TD6 601 A 1 HETATM 12 C C11 TD6 . . . B 2 41.83 -59.193 5.747 1 82.74 ? C11 TD6 601 A 1 HETATM 13 C C13 TD6 . . . B 2 43.939 -58.229 4.831 1 77.8 ? C13 TD6 601 A 1 HETATM 14 O O1A TD6 . . . B 2 43.895 -61.679 13.175 1 62 ? O1A TD6 601 A 1 HETATM 15 O O1B TD6 . . . B 2 43.705 -57.235 15.203 1 75.77 ? O1B TD6 601 A 1 HETATM 16 C C2' TD6 . . . B 2 41.849 -65.415 5.227 1 67.09 ? C2' TD6 601 A 1 HETATM 17 O O2A TD6 . . . B 2 42.381 -60.933 15.12 1 49.02 ? O2A TD6 601 A 1 HETATM 18 O O2B TD6 . . . B 2 41.422 -58.148 14.609 1 62.7 ? O2B TD6 601 A 1 HETATM 19 N N3' TD6 . . . B 2 42.635 -64.339 5.187 1 57.59 ? N3' TD6 601 A 1 HETATM 20 O O3A TD6 . . . B 2 43.425 -59.203 13.615 1 65.92 ? O3A TD6 601 A 1 HETATM 21 O O3B TD6 . . . B 2 42.715 -56.913 12.89 1 65.22 ? O3B TD6 601 A 1 HETATM 22 C C4' TD6 . . . B 2 42.048 -63.14 5.332 1 72.32 ? C4' TD6 601 A 1 HETATM 23 N N4' TD6 . . . B 2 42.863 -62.078 5.287 1 80.53 ? N4' TD6 601 A 1 HETATM 24 C C5' TD6 . . . B 2 40.652 -63.002 5.519 1 70.93 ? C5' TD6 601 A 1 HETATM 25 C C6' TD6 . . . B 2 39.943 -64.185 5.543 1 55 ? C6' TD6 601 A 1 HETATM 26 C C7' TD6 . . . B 2 39.957 -61.662 5.694 1 75.24 ? C7' TD6 601 A 1 HETATM 27 O OL1 TD6 . . . B 2 40.992 -58.123 5.286 1 55.8 ? OL1 TD6 601 A 1 HETATM 28 O OL2 TD6 . . . B 2 45.725 -56.861 4.088 1 71.22 ? OL2 TD6 601 A 1 HETATM 29 O OL3 TD6 . . . B 2 45.749 -57.485 6.211 1 74.6 ? OL3 TD6 601 A 1 HETATM 30 C CLB TD6 . . . B 2 43.227 -58.676 6.094 1 77.49 ? CLB TD6 601 A 1 HETATM 31 C CLC TD6 . . . B 2 45.233 -57.468 5.062 1 81.3 ? CLC TD6 601 A 1 HETATM 32 C CM2 TD6 . . . B 2 42.497 -66.751 5.064 1 48.07 ? CM2 TD6 601 A 1 HETATM 33 C CM4 TD6 . . . B 2 39.056 -62.511 8.425 1 65.65 ? CM4 TD6 601 A 1 # _model_server_stats.io_time_ms 85 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 351 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 33 #