data_5KNT # _model_server_result.job_id k0bjK3a4jgoP4TCAwhDtjg _model_server_result.datetime_utc '2024-10-20 13:00:59' _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 5knt # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 5KNT # _exptl.entry_id 5KNT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 361.291 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '2-[[(2~{S})-2,3-bis(oxidanyl)propyl]-[2-(6-oxidanylidene-1~{H}-purin-9-yl)ethyl]amino]ethylphosphonic acid' _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 5KNT _cell.length_a 84.655 _cell.length_b 84.655 _cell.length_c 166.819 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KNT _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 tetrameric 4 author_and_software_defined_assembly 1 PISA dimeric 2 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 1 1,2 A,B,C,D,E,F,G,H 2 1 # 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_554 x-y,-y,-z-1/3 1 0 0 0 -1 0 0 0 -1 0 0 -55.606333 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 E 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 163 A ASP 163 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.243 ? metalc ? metalc2 D MG MG . A MG 202 1_555 G O HOH . A HOH 367 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.097 ? metalc ? metalc3 D MG MG . A MG 202 1_555 G O HOH . A HOH 368 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? # _chem_comp.formula 'C12 H20 N5 O6 P' _chem_comp.formula_weight 361.291 _chem_comp.id 6WB _chem_comp.mon_nstd_flag . _chem_comp.name '2-[[(2~{S})-2,3-bis(oxidanyl)propyl]-[2-(6-oxidanylidene-1~{H}-purin-9-yl)ethyl]amino]ethylphosphonic acid' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms '2-((2,3-Dihydroxypropyl)(2-(hypoxanthin-9-yl)ethyl)amino)ethylphosphonic acid' # 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 OAE PAX 6WB doub 1 n n OAB PAX 6WB sing 2 n n PAX OAF 6WB sing 3 n n PAX CAM 6WB sing 4 n n CAK CAM 6WB sing 5 n n CAK NAV 6WB sing 6 n n CAU OAD 6WB sing 7 n n CAU CAI 6WB sing 8 n n CAU CAN 6WB sing 9 n n NAV CAN 6WB sing 10 n n NAV CAJ 6WB sing 11 n n CAI OAC 6WB sing 12 n n CAL CAJ 6WB sing 13 n n CAL N9 6WB sing 14 n n N9 C8 6WB sing 15 n y N9 C4 6WB sing 16 n y C8 N7 6WB doub 17 n y C4 N3 6WB sing 18 n n C4 C5 6WB doub 19 n y N3 C2 6WB doub 20 n n N7 C5 6WB sing 21 n y C5 C6 6WB sing 22 n n C2 N1 6WB sing 23 n n C6 N1 6WB sing 24 n n C6 O6 6WB doub 25 n n C8 H1 6WB sing 26 n n N1 H2 6WB sing 27 n n C2 H3 6WB sing 28 n n CAL H4 6WB sing 29 n n CAL H5 6WB sing 30 n n CAJ H6 6WB sing 31 n n CAJ H7 6WB sing 32 n n CAK H9 6WB sing 33 n n CAK H10 6WB sing 34 n n CAM H11 6WB sing 35 n n CAM H12 6WB sing 36 n n OAF H13 6WB sing 37 n n OAB H14 6WB sing 38 n n CAN H15 6WB sing 39 n n CAN H16 6WB sing 40 n n CAU H17 6WB sing 41 n n OAD H18 6WB sing 42 n n CAI H19 6WB sing 43 n n CAI H20 6WB sing 44 n n OAC H21 6WB sing 45 n n # _atom_sites.entry_id 5KNT _atom_sites.fract_transf_matrix[1][1] 0.011813 _atom_sites.fract_transf_matrix[1][2] 0.00682 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01364 _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] 0.005995 _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 6WB A 1 201 1 6WB DRG . D 3 MG A 1 202 1 MG MG . E 2 6WB B 1 201 2 6WB DRG . F 4 EPE B 1 202 1 EPE EPE . G 5 HOH A 1 301 62 HOH HOH . G 5 HOH A 2 302 152 HOH HOH . G 5 HOH A 3 303 106 HOH HOH . G 5 HOH A 4 304 153 HOH HOH . G 5 HOH A 5 305 103 HOH HOH . G 5 HOH A 6 306 10 HOH HOH . G 5 HOH A 7 307 92 HOH HOH . G 5 HOH A 8 308 150 HOH HOH . G 5 HOH A 9 309 169 HOH HOH . G 5 HOH A 10 310 102 HOH HOH . G 5 HOH A 11 311 149 HOH HOH . G 5 HOH A 12 312 86 HOH HOH . G 5 HOH A 13 313 16 HOH HOH . G 5 HOH A 14 314 147 HOH HOH . G 5 HOH A 15 315 77 HOH HOH . G 5 HOH A 16 316 12 HOH HOH . G 5 HOH A 17 317 132 HOH HOH . G 5 HOH A 18 318 43 HOH HOH . G 5 HOH A 19 319 8 HOH HOH . G 5 HOH A 20 320 58 HOH HOH . G 5 HOH A 21 321 2 HOH HOH . G 5 HOH A 22 322 49 HOH HOH . G 5 HOH A 23 323 6 HOH HOH . G 5 HOH A 24 324 48 HOH HOH . G 5 HOH A 25 325 141 HOH HOH . G 5 HOH A 26 326 28 HOH HOH . G 5 HOH A 27 327 7 HOH HOH . G 5 HOH A 28 328 3 HOH HOH . G 5 HOH A 29 329 146 HOH HOH . G 5 HOH A 30 330 110 HOH HOH . G 5 HOH A 31 331 72 HOH HOH . G 5 HOH A 32 332 69 HOH HOH . G 5 HOH A 33 333 19 HOH HOH . G 5 HOH A 34 334 180 HOH HOH . G 5 HOH A 35 335 179 HOH HOH . G 5 HOH A 36 336 80 HOH HOH . G 5 HOH A 37 337 203 HOH HOH . G 5 HOH A 38 338 21 HOH HOH . G 5 HOH A 39 339 91 HOH HOH . G 5 HOH A 40 340 54 HOH HOH . G 5 HOH A 41 341 137 HOH HOH . G 5 HOH A 42 342 20 HOH HOH . G 5 HOH A 43 343 37 HOH HOH . G 5 HOH A 44 344 68 HOH HOH . G 5 HOH A 45 345 148 HOH HOH . G 5 HOH A 46 346 46 HOH HOH . G 5 HOH A 47 347 138 HOH HOH . G 5 HOH A 48 348 126 HOH HOH . G 5 HOH A 49 349 83 HOH HOH . G 5 HOH A 50 350 24 HOH HOH . G 5 HOH A 51 351 13 HOH HOH . G 5 HOH A 52 352 59 HOH HOH . G 5 HOH A 53 353 194 HOH HOH . G 5 HOH A 54 354 42 HOH HOH . G 5 HOH A 55 355 181 HOH HOH . G 5 HOH A 56 356 65 HOH HOH . G 5 HOH A 57 357 174 HOH HOH . G 5 HOH A 58 358 200 HOH HOH . G 5 HOH A 59 359 70 HOH HOH . G 5 HOH A 60 360 151 HOH HOH . G 5 HOH A 61 361 17 HOH HOH . G 5 HOH A 62 362 129 HOH HOH . G 5 HOH A 63 363 192 HOH HOH . G 5 HOH A 64 364 67 HOH HOH . G 5 HOH A 65 365 155 HOH HOH . G 5 HOH A 66 366 204 HOH HOH . G 5 HOH A 67 367 198 HOH HOH . G 5 HOH A 68 368 199 HOH HOH . G 5 HOH A 69 369 135 HOH HOH . G 5 HOH A 70 370 175 HOH HOH . G 5 HOH A 71 371 185 HOH HOH . G 5 HOH A 72 372 205 HOH HOH . G 5 HOH A 73 373 119 HOH HOH . G 5 HOH A 74 374 104 HOH HOH . G 5 HOH A 75 375 63 HOH HOH . G 5 HOH A 76 376 162 HOH HOH . G 5 HOH A 77 377 191 HOH HOH . G 5 HOH A 78 378 144 HOH HOH . G 5 HOH A 79 379 111 HOH HOH . G 5 HOH A 80 380 105 HOH HOH . G 5 HOH A 81 381 85 HOH HOH . G 5 HOH A 82 382 120 HOH HOH . G 5 HOH A 83 383 93 HOH HOH . G 5 HOH A 84 384 136 HOH HOH . G 5 HOH A 85 385 56 HOH HOH . G 5 HOH A 86 386 97 HOH HOH . G 5 HOH A 87 387 133 HOH HOH . G 5 HOH A 88 388 123 HOH HOH . G 5 HOH A 89 389 36 HOH HOH . G 5 HOH A 90 390 166 HOH HOH . G 5 HOH A 91 391 196 HOH HOH . G 5 HOH A 92 392 168 HOH HOH . G 5 HOH A 93 393 190 HOH HOH . G 5 HOH A 94 394 167 HOH HOH . G 5 HOH A 95 395 161 HOH HOH . H 5 HOH B 1 301 87 HOH HOH . H 5 HOH B 2 302 4 HOH HOH . H 5 HOH B 3 303 45 HOH HOH . H 5 HOH B 4 304 35 HOH HOH . H 5 HOH B 5 305 1 HOH HOH . H 5 HOH B 6 306 60 HOH HOH . H 5 HOH B 7 307 57 HOH HOH . H 5 HOH B 8 308 14 HOH HOH . H 5 HOH B 9 309 26 HOH HOH . H 5 HOH B 10 310 31 HOH HOH . H 5 HOH B 11 311 66 HOH HOH . H 5 HOH B 12 312 5 HOH HOH . H 5 HOH B 13 313 78 HOH HOH . H 5 HOH B 14 314 131 HOH HOH . H 5 HOH B 15 315 128 HOH HOH . H 5 HOH B 16 316 25 HOH HOH . H 5 HOH B 17 317 99 HOH HOH . H 5 HOH B 18 318 50 HOH HOH . H 5 HOH B 19 319 201 HOH HOH . H 5 HOH B 20 320 108 HOH HOH . H 5 HOH B 21 321 41 HOH HOH . H 5 HOH B 22 322 39 HOH HOH . H 5 HOH B 23 323 18 HOH HOH . H 5 HOH B 24 324 89 HOH HOH . H 5 HOH B 25 325 82 HOH HOH . H 5 HOH B 26 326 115 HOH HOH . H 5 HOH B 27 327 51 HOH HOH . H 5 HOH B 28 328 88 HOH HOH . H 5 HOH B 29 329 15 HOH HOH . H 5 HOH B 30 330 30 HOH HOH . H 5 HOH B 31 331 116 HOH HOH . H 5 HOH B 32 332 9 HOH HOH . H 5 HOH B 33 333 38 HOH HOH . H 5 HOH B 34 334 11 HOH HOH . H 5 HOH B 35 335 44 HOH HOH . H 5 HOH B 36 336 139 HOH HOH . H 5 HOH B 37 337 55 HOH HOH . H 5 HOH B 38 338 53 HOH HOH . H 5 HOH B 39 339 29 HOH HOH . H 5 HOH B 40 340 109 HOH HOH . H 5 HOH B 41 341 171 HOH HOH . H 5 HOH B 42 342 177 HOH HOH . H 5 HOH B 43 343 189 HOH HOH . H 5 HOH B 44 344 23 HOH HOH . H 5 HOH B 45 345 101 HOH HOH . H 5 HOH B 46 346 130 HOH HOH . H 5 HOH B 47 347 154 HOH HOH . H 5 HOH B 48 348 32 HOH HOH . H 5 HOH B 49 349 193 HOH HOH . H 5 HOH B 50 350 100 HOH HOH . H 5 HOH B 51 351 22 HOH HOH . H 5 HOH B 52 352 122 HOH HOH . H 5 HOH B 53 353 76 HOH HOH . H 5 HOH B 54 354 178 HOH HOH . H 5 HOH B 55 355 74 HOH HOH . H 5 HOH B 56 356 197 HOH HOH . H 5 HOH B 57 357 188 HOH HOH . H 5 HOH B 58 358 195 HOH HOH . H 5 HOH B 59 359 184 HOH HOH . H 5 HOH B 60 360 172 HOH HOH . H 5 HOH B 61 361 140 HOH HOH . H 5 HOH B 62 362 170 HOH HOH . H 5 HOH B 63 363 84 HOH HOH . H 5 HOH B 64 364 75 HOH HOH . H 5 HOH B 65 365 98 HOH HOH . H 5 HOH B 66 366 96 HOH HOH . H 5 HOH B 67 367 64 HOH HOH . H 5 HOH B 68 368 113 HOH HOH . H 5 HOH B 69 369 73 HOH HOH . H 5 HOH B 70 370 202 HOH HOH . H 5 HOH B 71 371 157 HOH HOH . H 5 HOH B 72 372 173 HOH HOH . H 5 HOH B 73 373 145 HOH HOH . H 5 HOH B 74 374 165 HOH HOH . H 5 HOH B 75 375 71 HOH HOH . H 5 HOH B 76 376 156 HOH HOH . H 5 HOH B 77 377 107 HOH HOH . H 5 HOH B 78 378 125 HOH HOH . H 5 HOH B 79 379 33 HOH HOH . H 5 HOH B 80 380 159 HOH HOH . H 5 HOH B 81 381 187 HOH HOH . H 5 HOH B 82 382 94 HOH HOH . H 5 HOH B 83 383 164 HOH HOH . H 5 HOH B 84 384 182 HOH HOH . H 5 HOH B 85 385 142 HOH HOH . H 5 HOH B 86 386 160 HOH HOH . H 5 HOH B 87 387 127 HOH HOH . H 5 HOH B 88 388 143 HOH HOH . H 5 HOH B 89 389 158 HOH HOH . H 5 HOH B 90 390 176 HOH HOH . H 5 HOH B 91 391 34 HOH HOH . H 5 HOH B 92 392 61 HOH HOH . H 5 HOH B 93 393 163 HOH HOH . H 5 HOH B 94 394 118 HOH HOH . H 5 HOH B 95 395 40 HOH HOH . H 5 HOH B 96 396 95 HOH HOH . H 5 HOH B 97 397 52 HOH HOH . H 5 HOH B 98 398 121 HOH HOH . H 5 HOH B 99 399 27 HOH HOH . H 5 HOH B 100 400 124 HOH HOH . H 5 HOH B 101 401 79 HOH HOH . H 5 HOH B 102 402 186 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 C C4 6WB . . . C 2 26.932 -9.628 -12.436 1 57.61 ? C4 6WB 201 A 1 HETATM 2 C C5 6WB . . . C 2 26.12 -10.181 -11.397 1 49.72 ? C5 6WB 201 A 1 HETATM 3 C C6 6WB . . . C 2 25.838 -9.357 -10.25 1 51.66 ? C6 6WB 201 A 1 HETATM 4 C C8 6WB . . . C 2 26.379 -11.675 -13.002 1 53.1 ? C8 6WB 201 A 1 HETATM 5 N N1 6WB . . . C 2 26.352 -8.101 -10.218 1 46.49 ? N1 6WB 201 A 1 HETATM 6 N N3 6WB . . . C 2 27.411 -8.336 -12.312 1 43.19 ? N3 6WB 201 A 1 HETATM 7 O O6 6WB . . . C 2 25.162 -9.77 -9.349 1 48.15 ? O6 6WB 201 A 1 HETATM 8 C C2 6WB . . . C 2 27.115 -7.618 -11.227 1 51.67 ? C2 6WB 201 A 1 HETATM 9 N N7 6WB . . . C 2 25.808 -11.464 -11.81 1 49.21 ? N7 6WB 201 A 1 HETATM 10 N N9 6WB . . . C 2 27.076 -10.59 -13.419 1 53.09 ? N9 6WB 201 A 1 HETATM 11 C CAL 6WB . . . C 2 27.797 -10.485 -14.648 1 43.39 ? CAL 6WB 201 A 1 HETATM 12 C CAJ 6WB . . . C 2 29.32 -10.818 -14.496 1 44.22 ? CAJ 6WB 201 A 1 HETATM 13 N NAV 6WB . . . C 2 30.001 -10.783 -15.744 1 57.14 ? NAV 6WB 201 A 1 HETATM 14 C CAK 6WB . . . C 2 29.668 -11.96 -16.556 1 53.74 ? CAK 6WB 201 A 1 HETATM 15 C CAM 6WB . . . C 2 30.37 -13.202 -16.011 1 54.57 ? CAM 6WB 201 A 1 HETATM 16 P PAX 6WB . . . C 2 29.988 -14.684 -17.02 1 59.53 ? PAX 6WB 201 A 1 HETATM 17 O OAE 6WB . . . C 2 30.58 -14.522 -18.4 1 53.13 ? OAE 6WB 201 A 1 HETATM 18 O OAF 6WB . . . C 2 30.564 -15.865 -16.396 1 43.74 ? OAF 6WB 201 A 1 HETATM 19 O OAB 6WB . . . C 2 28.474 -14.856 -17.104 1 45.43 ? OAB 6WB 201 A 1 HETATM 20 C CAN 6WB . . . C 2 31.445 -10.767 -15.535 1 56.3 ? CAN 6WB 201 A 1 HETATM 21 C CAU 6WB . . . C 2 32.071 -9.543 -16.242 1 69.76 ? CAU 6WB 201 A 1 HETATM 22 O OAD 6WB . . . C 2 33.505 -9.583 -16.084 1 78.27 ? OAD 6WB 201 A 1 HETATM 23 C CAI 6WB . . . C 2 31.573 -8.346 -15.607 1 59.66 ? CAI 6WB 201 A 1 HETATM 24 O OAC 6WB . . . C 2 32.192 -8.282 -14.318 1 66.5 ? OAC 6WB 201 A 1 # _model_server_stats.io_time_ms 15 _model_server_stats.parse_time_ms 36 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 491 _model_server_stats.encode_time_ms 8 _model_server_stats.element_count 24 #