data_2F17 # _model_server_result.job_id CTd4b4X6BthPg4SsIRMy6A _model_server_result.datetime_utc '2024-12-22 08:17:45' _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 2f17 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"N","auth_seq_id":2202}' # _entry.id 2F17 # _exptl.entry_id 2F17 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 419.287 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM _entity.pdbx_number_of_molecules 2 _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 2F17 _cell.length_a 89.363 _cell.length_b 89.363 _cell.length_c 141.43 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2F17 _symmetry.cell_setting ? _symmetry.Int_Tables_number 152 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 31 2 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 tetrameric 4 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,C,D,E,F,G,H,I,J,K,L,M,N,O,P 1 1 A,B,C,D,E,F,G,H,I,J,K,L,M,N,O,P 2 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' 5_675 x-y+1,-y+2,-z+2/3 1 0 0 0 -1 0 0 0 -1 0 154.781256 94.286667 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 4 I N N ? 4 N N 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 OD2 ASP 66 A ASP 46 1_555 C MG MG . A MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.409 ? metalc ? metalc2 A OD1 ASP 91 A ASP 71 1_555 C MG MG . A MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.396 ? metalc ? metalc3 A OD1 ASP 93 A ASP 73 1_555 C MG MG . A MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.398 ? metalc ? metalc4 A OD2 ASP 120 A ASP 100 1_555 C MG MG . A MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.414 ? metalc ? metalc5 J O3P AMP . A AMP 301 1_555 C MG MG . A MG 901 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.404 ? metalc ? metalc6 C MG MG . A MG 901 1_555 I O2A PYI . A PYI 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc7 B OD2 ASP 66 B ASP 46 1_555 K MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.401 ? metalc ? metalc8 B OD2 ASP 91 B ASP 71 1_555 K MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.42 ? metalc ? metalc9 B OD2 ASP 120 B ASP 100 1_555 K MG MG . B MG 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.403 ? metalc ? metalc10 K MG MG . B MG 902 1_555 M O2S EPE . B EPE 2201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.423 ? metalc ? metalc11 K MG MG . B MG 902 1_555 N O2A PYI . B PYI 2202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? metalc ? metalc12 K MG MG . B MG 902 1_555 N O2B PYI . B PYI 2202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.446 ? # _chem_comp.formula 'C14 H21 N4 O7 P2 1' _chem_comp.formula_weight 419.287 _chem_comp.id PYI _chem_comp.mon_nstd_flag . _chem_comp.name 1-[(4-AMINO-2-METHYLPYRIMIDIN-5-YL)METHYL]-3-(2-{[HYDROXY(PHOSPHONOOXY)PHOSPHORYL]OXY}ETHYL)-2-METHYLPYRIDINIUM _chem_comp.type non-polymer _chem_comp.pdbx_synonyms 'PYRITHIAMIN PYROPHOSPHATE' # 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 CM2 C2A PYI sing 349 n n CM2 HM21 PYI sing 350 n n CM2 HM22 PYI sing 351 n n CM2 HM23 PYI sing 352 n n C2A N1A PYI doub 353 n y C2A N3A PYI sing 354 n y N1A C6A PYI sing 355 n y C6A C5A PYI doub 356 n y C6A H6A PYI sing 357 n n C5A C7A PYI sing 358 n n C5A C4A PYI sing 359 n y C7A N3 PYI sing 360 n n C7A H7A1 PYI sing 361 n n C7A H7A2 PYI sing 362 n n N3 C2 PYI doub 363 n y N3 C4 PYI sing 364 n y C2 C1 PYI sing 365 n y C2 H2 PYI sing 366 n n C1 C6 PYI doub 367 n y C1 H1 PYI sing 368 n n C6 C5 PYI sing 369 n y C6 H6 PYI sing 370 n n C5 CM6 PYI sing 371 n n C5 C4 PYI doub 372 n y CM6 CM7 PYI sing 373 n n CM6 HM61 PYI sing 374 n n CM6 HM62 PYI sing 375 n n CM7 OM7 PYI sing 376 n n CM7 HM71 PYI sing 377 n n CM7 HM72 PYI sing 378 n n OM7 PA PYI sing 379 n n PA O1A PYI doub 380 n n PA O2A PYI sing 381 n n PA O3A PYI sing 382 n n O2A H2A PYI sing 383 n n O3A PB PYI sing 384 n n PB O1B PYI doub 385 n n PB O2B PYI sing 386 n n PB O3B PYI sing 387 n n O2B H2B PYI sing 388 n n O3B H3B PYI sing 389 n n C4 CM4 PYI sing 390 n n CM4 HM41 PYI sing 391 n n CM4 HM42 PYI sing 392 n n CM4 HM43 PYI sing 393 n n C4A N4A PYI sing 394 n n C4A N3A PYI doub 395 n y N4A H4A1 PYI sing 396 n n N4A H4A2 PYI sing 397 n n # _atom_sites.entry_id 2F17 _atom_sites.fract_transf_matrix[1][1] 0.01119 _atom_sites.fract_transf_matrix[1][2] 0.006461 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012921 _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] 0.007071 _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 C 2 MG A 1 901 901 MG MG . D 3 SO4 A 1 401 401 SO4 SO4 . E 3 SO4 A 1 403 403 SO4 SO4 . F 3 SO4 A 1 404 404 SO4 SO4 . G 3 SO4 A 1 405 405 SO4 SO4 . H 3 SO4 A 1 406 406 SO4 SO4 . I 4 PYI A 1 902 201 PYI PYI . J 5 AMP A 1 301 301 AMP AMP . K 2 MG B 1 902 902 MG MG . L 3 SO4 B 1 402 402 SO4 SO4 . M 6 EPE B 1 2201 2201 EPE EPE . N 4 PYI B 1 2202 202 PYI PYI . O 7 HOH A 1 903 3 HOH TIP . O 7 HOH A 2 904 4 HOH TIP . O 7 HOH A 3 905 5 HOH TIP . O 7 HOH A 4 906 7 HOH TIP . O 7 HOH A 5 907 9 HOH TIP . O 7 HOH A 6 908 10 HOH TIP . O 7 HOH A 7 909 11 HOH TIP . O 7 HOH A 8 910 23 HOH TIP . O 7 HOH A 9 911 24 HOH TIP . O 7 HOH A 10 912 25 HOH TIP . O 7 HOH A 11 913 27 HOH TIP . O 7 HOH A 12 914 30 HOH TIP . O 7 HOH A 13 915 32 HOH TIP . O 7 HOH A 14 916 33 HOH TIP . O 7 HOH A 15 917 37 HOH TIP . O 7 HOH A 16 918 38 HOH TIP . O 7 HOH A 17 919 40 HOH TIP . O 7 HOH A 18 920 41 HOH TIP . O 7 HOH A 19 921 43 HOH TIP . O 7 HOH A 20 922 44 HOH TIP . O 7 HOH A 21 923 48 HOH TIP . O 7 HOH A 22 924 53 HOH TIP . O 7 HOH A 23 925 55 HOH TIP . O 7 HOH A 24 926 56 HOH TIP . O 7 HOH A 25 927 57 HOH TIP . O 7 HOH A 26 928 64 HOH TIP . O 7 HOH A 27 929 65 HOH TIP . O 7 HOH A 28 930 67 HOH TIP . O 7 HOH A 29 931 70 HOH TIP . O 7 HOH A 30 932 72 HOH TIP . O 7 HOH A 31 933 73 HOH TIP . O 7 HOH A 32 934 75 HOH TIP . O 7 HOH A 33 935 76 HOH TIP . O 7 HOH A 34 936 78 HOH TIP . O 7 HOH A 35 937 79 HOH TIP . O 7 HOH A 36 938 80 HOH TIP . O 7 HOH A 37 939 84 HOH TIP . O 7 HOH A 38 940 85 HOH TIP . O 7 HOH A 39 941 86 HOH TIP . O 7 HOH A 40 942 88 HOH TIP . O 7 HOH A 41 943 89 HOH TIP . O 7 HOH A 42 944 90 HOH TIP . O 7 HOH A 43 945 94 HOH TIP . O 7 HOH A 44 946 96 HOH TIP . O 7 HOH A 45 947 98 HOH TIP . O 7 HOH A 46 948 99 HOH TIP . O 7 HOH A 47 949 100 HOH TIP . O 7 HOH A 48 950 106 HOH TIP . O 7 HOH A 49 951 107 HOH TIP . O 7 HOH A 50 952 109 HOH TIP . O 7 HOH A 51 953 112 HOH TIP . O 7 HOH A 52 954 113 HOH TIP . O 7 HOH A 53 955 114 HOH TIP . O 7 HOH A 54 956 115 HOH TIP . O 7 HOH A 55 957 116 HOH TIP . O 7 HOH A 56 958 120 HOH TIP . O 7 HOH A 57 959 122 HOH TIP . O 7 HOH A 58 960 126 HOH TIP . O 7 HOH A 59 961 127 HOH TIP . O 7 HOH A 60 962 130 HOH TIP . O 7 HOH A 61 963 132 HOH TIP . P 7 HOH B 1 2203 1 HOH TIP . P 7 HOH B 2 2204 2 HOH TIP . P 7 HOH B 3 2205 6 HOH TIP . P 7 HOH B 4 2206 8 HOH TIP . P 7 HOH B 5 2207 12 HOH TIP . P 7 HOH B 6 2208 13 HOH TIP . P 7 HOH B 7 2209 14 HOH TIP . P 7 HOH B 8 2210 15 HOH TIP . P 7 HOH B 9 2211 16 HOH TIP . P 7 HOH B 10 2212 17 HOH TIP . P 7 HOH B 11 2213 18 HOH TIP . P 7 HOH B 12 2214 19 HOH TIP . P 7 HOH B 13 2215 20 HOH TIP . P 7 HOH B 14 2216 21 HOH TIP . P 7 HOH B 15 2217 22 HOH TIP . P 7 HOH B 16 2218 26 HOH TIP . P 7 HOH B 17 2219 28 HOH TIP . P 7 HOH B 18 2220 29 HOH TIP . P 7 HOH B 19 2221 31 HOH TIP . P 7 HOH B 20 2222 34 HOH TIP . P 7 HOH B 21 2223 35 HOH TIP . P 7 HOH B 22 2224 36 HOH TIP . P 7 HOH B 23 2225 39 HOH TIP . P 7 HOH B 24 2226 42 HOH TIP . P 7 HOH B 25 2227 45 HOH TIP . P 7 HOH B 26 2228 46 HOH TIP . P 7 HOH B 27 2229 47 HOH TIP . P 7 HOH B 28 2230 49 HOH TIP . P 7 HOH B 29 2231 50 HOH TIP . P 7 HOH B 30 2232 51 HOH TIP . P 7 HOH B 31 2233 52 HOH TIP . P 7 HOH B 32 2234 54 HOH TIP . P 7 HOH B 33 2235 58 HOH TIP . P 7 HOH B 34 2236 59 HOH TIP . P 7 HOH B 35 2237 60 HOH TIP . P 7 HOH B 36 2238 61 HOH TIP . P 7 HOH B 37 2239 62 HOH TIP . P 7 HOH B 38 2240 63 HOH TIP . P 7 HOH B 39 2241 66 HOH TIP . P 7 HOH B 40 2242 68 HOH TIP . P 7 HOH B 41 2243 69 HOH TIP . P 7 HOH B 42 2244 71 HOH TIP . P 7 HOH B 43 2245 74 HOH TIP . P 7 HOH B 44 2246 77 HOH TIP . P 7 HOH B 45 2247 81 HOH TIP . P 7 HOH B 46 2248 82 HOH TIP . P 7 HOH B 47 2249 83 HOH TIP . P 7 HOH B 48 2250 87 HOH TIP . P 7 HOH B 49 2251 91 HOH TIP . P 7 HOH B 50 2252 92 HOH TIP . P 7 HOH B 51 2253 93 HOH TIP . P 7 HOH B 52 2254 95 HOH TIP . P 7 HOH B 53 2255 97 HOH TIP . P 7 HOH B 54 2256 101 HOH TIP . P 7 HOH B 55 2257 102 HOH TIP . P 7 HOH B 56 2258 103 HOH TIP . P 7 HOH B 57 2259 104 HOH TIP . P 7 HOH B 58 2260 105 HOH TIP . P 7 HOH B 59 2261 108 HOH TIP . P 7 HOH B 60 2262 110 HOH TIP . P 7 HOH B 61 2263 111 HOH TIP . P 7 HOH B 62 2264 117 HOH TIP . P 7 HOH B 63 2265 118 HOH TIP . P 7 HOH B 64 2266 119 HOH TIP . P 7 HOH B 65 2267 121 HOH TIP . P 7 HOH B 66 2268 123 HOH TIP . P 7 HOH B 67 2269 124 HOH TIP . P 7 HOH B 68 2270 125 HOH TIP . P 7 HOH B 69 2271 128 HOH TIP . P 7 HOH B 70 2272 129 HOH TIP . P 7 HOH B 71 2273 131 HOH TIP . # 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 C CM2 PYI . . . N 4 6.847 69.455 25.418 1 33.88 ? CM2 PYI 2202 B 1 HETATM 2 C C2A PYI . . . N 4 6.831 69.863 23.969 1 33.6 ? C2A PYI 2202 B 1 HETATM 3 N N1A PYI . . . N 4 7.958 69.791 23.262 1 34.63 ? N1A PYI 2202 B 1 HETATM 4 C C6A PYI . . . N 4 7.996 70.145 21.964 1 35.17 ? C6A PYI 2202 B 1 HETATM 5 C C5A PYI . . . N 4 6.83 70.601 21.334 1 36.19 ? C5A PYI 2202 B 1 HETATM 6 C C7A PYI . . . N 4 6.862 71.008 19.868 1 38.86 ? C7A PYI 2202 B 1 HETATM 7 N N3 PYI . . . N 4 6.222 70.048 18.906 1 41.5 ? N3 PYI 2202 B 1 HETATM 8 C C2 PYI . . . N 4 5.941 68.776 19.293 1 42.95 ? C2 PYI 2202 B 1 HETATM 9 C C1 PYI . . . N 4 5.356 67.853 18.43 1 43.82 ? C1 PYI 2202 B 1 HETATM 10 C C6 PYI . . . N 4 5.055 68.25 17.125 1 45.92 ? C6 PYI 2202 B 1 HETATM 11 C C5 PYI . . . N 4 5.341 69.567 16.706 1 47.06 ? C5 PYI 2202 B 1 HETATM 12 C CM6 PYI . . . N 4 5.013 69.959 15.286 1 52.12 ? CM6 PYI 2202 B 1 HETATM 13 C CM7 PYI . . . N 4 6.208 69.575 14.405 1 58.35 ? CM7 PYI 2202 B 1 HETATM 14 O OM7 PYI . . . N 4 5.794 68.604 13.443 1 65 ? OM7 PYI 2202 B 1 HETATM 15 P PA PYI . . . N 4 6.337 69.077 11.999 1 68.31 ? PA PYI 2202 B 1 HETATM 16 O O1A PYI . . . N 4 6.229 67.879 11.047 1 68.94 ? O1A PYI 2202 B 1 HETATM 17 O O2A PYI . . . N 4 5.452 70.231 11.458 1 68.06 ? O2A PYI 2202 B 1 HETATM 18 O O3A PYI . . . N 4 7.914 69.496 12.155 1 70 ? O3A PYI 2202 B 1 HETATM 19 P PB PYI . . . N 4 8.353 70.714 11.179 1 72.43 ? PB PYI 2202 B 1 HETATM 20 O O1B PYI . . . N 4 9.823 70.456 10.717 1 72.79 ? O1B PYI 2202 B 1 HETATM 21 O O2B PYI . . . N 4 7.444 70.792 9.907 1 72.46 ? O2B PYI 2202 B 1 HETATM 22 O O3B PYI . . . N 4 8.3 72.081 11.952 1 72.96 ? O3B PYI 2202 B 1 HETATM 23 C C4 PYI . . . N 4 5.938 70.477 17.636 1 44.32 ? C4 PYI 2202 B 1 HETATM 24 C CM4 PYI . . . N 4 6.262 71.915 17.212 1 43.5 ? CM4 PYI 2202 B 1 HETATM 25 C C4A PYI . . . N 4 5.644 70.667 22.116 1 34.68 ? C4A PYI 2202 B 1 HETATM 26 N N4A PYI . . . N 4 4.457 71.108 21.556 1 32.56 ? N4A PYI 2202 B 1 HETATM 27 N N3A PYI . . . N 4 5.692 70.292 23.414 1 34.28 ? N3A PYI 2202 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 24 _model_server_stats.query_time_ms 264 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 27 #