data_5ETM # _model_server_result.job_id iPqVLnvuPkBRZmYnxVaC8Q _model_server_result.datetime_utc '2024-10-15 14:31:00' _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 5etm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 5ETM # _exptl.entry_id 5ETM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 505.208 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _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 115.49 _cell.angle_gamma 90 _cell.entry_id 5ETM _cell.length_a 35.763 _cell.length_b 57.631 _cell.length_c 38.407 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5ETM _symmetry.cell_setting ? _symmetry.Int_Tables_number 4 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 1 21 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,F,G,H,I,J _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 GLY 30 A GLY 26 1_555 G NA NA . A NA 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.858 ? metalc ? metalc2 A O ILE 32 A ILE 28 1_555 G NA NA . A NA 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.304 ? metalc ? metalc3 A O SER 35 A SER 31 1_555 G NA NA . A NA 206 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc4 A O LEU 38 A LEU 34 1_555 F NA NA . A NA 205 2_545 ? ? ? ? ? ? ? ? ? ? ? ? 2.335 ? metalc ? metalc5 A OD1 ASP 53 A ASP 49 1_555 F NA NA . A NA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.542 ? metalc ? metalc6 A OD2 ASP 53 A ASP 49 1_555 F NA NA . A NA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc7 A OE1 GLU 91 A GLU 87 1_555 F NA NA . A NA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 3.075 ? metalc ? metalc8 A OE2 GLU 91 A GLU 87 1_555 F NA NA . A NA 205 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.777 ? metalc ? metalc9 A OD1 ASP 99 A ASP 95 1_555 D CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.338 ? metalc ? metalc10 A OD2 ASP 99 A ASP 95 1_555 E CA CA . A CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.329 ? metalc ? metalc11 A OD1 ASP 101 A ASP 97 1_555 D CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.292 ? metalc ? metalc12 A OD2 ASP 101 A ASP 97 1_555 E CA CA . A CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.342 ? metalc ? metalc13 A OE2 GLU 113 A GLU 109 1_555 G NA NA . A NA 206 2_454 ? ? ? ? ? ? ? ? ? ? ? ? 2.362 ? metalc ? metalc14 C O1B APC . A APC 202 1_555 D CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.35 ? metalc ? metalc15 C O1A APC . A APC 202 1_555 D CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.309 ? metalc ? metalc16 C O2G APC . A APC 202 1_555 E CA CA . A CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.347 ? metalc ? metalc17 C O1B APC . A APC 202 1_555 E CA CA . A CA 204 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc18 D CA CA . A CA 203 1_555 J O HOH . A HOH 332 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.339 ? metalc ? metalc19 D CA CA . A CA 203 1_555 J O HOH . A HOH 363 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.283 ? metalc ? metalc20 E CA CA . A CA 204 1_555 J O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.38 ? metalc ? metalc21 E CA CA . A CA 204 1_555 J O HOH . A HOH 370 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc22 F NA NA . A NA 205 1_555 J O HOH . A HOH 308 2_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.172 ? metalc ? metalc23 F NA NA . A NA 205 1_555 J O HOH . A HOH 348 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.307 ? metalc ? metalc24 G NA NA . A NA 206 1_555 J O HOH . A HOH 317 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.779 ? metalc ? metalc25 G NA NA . A NA 206 1_555 J O HOH . A HOH 353 2_444 ? ? ? ? ? ? ? ? ? ? ? ? 2.341 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id APC _chem_comp.mon_nstd_flag . _chem_comp.name 'DIPHOSPHOMETHYLPHOSPHONIC ACID ADENOSYL ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA,BETA-METHYLENEADENOSINE-5'-TRIPHOSPHATE" # 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 PG O1G APC doub 45 n n PG O2G APC sing 46 n n PG O3G APC sing 47 n n PG O3B APC sing 48 n n O2G HOG2 APC sing 49 n n O3G HOG3 APC sing 50 n n PB O1B APC doub 51 n n PB O2B APC sing 52 n n PB O3B APC sing 53 n n PB C3A APC sing 54 n n O2B HOB2 APC sing 55 n n PA O1A APC doub 56 n n PA O2A APC sing 57 n n PA C3A APC sing 58 n n PA O5' APC sing 59 n n O2A HOA2 APC sing 60 n n C3A H3A1 APC sing 61 n n C3A H3A2 APC sing 62 n n O5' C5' APC sing 63 n n C5' C4' APC sing 64 n n C5' "H5'1" APC sing 65 n n C5' "H5'2" APC sing 66 n n C4' O4' APC sing 67 n n C4' C3' APC sing 68 n n C4' H4' APC sing 69 n n O4' C1' APC sing 70 n n C3' O3' APC sing 71 n n C3' C2' APC sing 72 n n C3' H3' APC sing 73 n n O3' HO3' APC sing 74 n n C2' O2' APC sing 75 n n C2' C1' APC sing 76 n n C2' H2' APC sing 77 n n O2' HO2' APC sing 78 n n C1' N9 APC sing 79 n n C1' H1' APC sing 80 n n N9 C8 APC sing 81 n y N9 C4 APC sing 82 n y C8 N7 APC doub 83 n y C8 H8 APC sing 84 n n N7 C5 APC sing 85 n y C5 C6 APC sing 86 n y C5 C4 APC doub 87 n y C6 N6 APC sing 88 n n C6 N1 APC doub 89 n y N6 HN61 APC sing 90 n n N6 HN62 APC sing 91 n n N1 C2 APC sing 92 n y C2 N3 APC doub 93 n y C2 H2 APC sing 94 n n N3 C4 APC sing 95 n y # _atom_sites.entry_id 5ETM _atom_sites.fract_transf_matrix[1][1] 0.027962 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.013328 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.017352 _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] 0.028844 _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 5RW A 1 201 1 5RW UNL . C 3 APC A 1 202 1 APC APC . D 4 CA A 1 203 1 CA CA . E 4 CA A 1 204 2 CA CA . F 5 NA A 1 205 1 NA NA . G 5 NA A 1 206 2 NA NA . H 6 CL A 1 207 1 CL CL . I 6 CL A 1 208 2 CL CL . J 7 HOH A 1 301 30 HOH HOH . J 7 HOH A 2 302 55 HOH HOH . J 7 HOH A 3 303 32 HOH HOH . J 7 HOH A 4 304 23 HOH HOH . J 7 HOH A 5 305 10 HOH HOH . J 7 HOH A 6 306 38 HOH HOH . J 7 HOH A 7 307 44 HOH HOH . J 7 HOH A 8 308 4 HOH HOH . J 7 HOH A 9 309 26 HOH HOH . J 7 HOH A 10 310 53 HOH HOH . J 7 HOH A 11 311 54 HOH HOH . J 7 HOH A 12 312 63 HOH HOH . J 7 HOH A 13 313 69 HOH HOH . J 7 HOH A 14 314 66 HOH HOH . J 7 HOH A 15 315 6 HOH HOH . J 7 HOH A 16 316 31 HOH HOH . J 7 HOH A 17 317 36 HOH HOH . J 7 HOH A 18 318 48 HOH HOH . J 7 HOH A 19 319 67 HOH HOH . J 7 HOH A 20 320 76 HOH HOH . J 7 HOH A 21 321 58 HOH HOH . J 7 HOH A 22 322 50 HOH HOH . J 7 HOH A 23 323 72 HOH HOH . J 7 HOH A 24 324 81 HOH HOH . J 7 HOH A 25 325 46 HOH HOH . J 7 HOH A 26 326 82 HOH HOH . J 7 HOH A 27 327 45 HOH HOH . J 7 HOH A 28 328 33 HOH HOH . J 7 HOH A 29 329 41 HOH HOH . J 7 HOH A 30 330 65 HOH HOH . J 7 HOH A 31 331 8 HOH HOH . J 7 HOH A 32 332 3 HOH HOH . J 7 HOH A 33 333 34 HOH HOH . J 7 HOH A 34 334 20 HOH HOH . J 7 HOH A 35 335 77 HOH HOH . J 7 HOH A 36 336 18 HOH HOH . J 7 HOH A 37 337 28 HOH HOH . J 7 HOH A 38 338 2 HOH HOH . J 7 HOH A 39 339 24 HOH HOH . J 7 HOH A 40 340 11 HOH HOH . J 7 HOH A 41 341 13 HOH HOH . J 7 HOH A 42 342 60 HOH HOH . J 7 HOH A 43 343 80 HOH HOH . J 7 HOH A 44 344 59 HOH HOH . J 7 HOH A 45 345 16 HOH HOH . J 7 HOH A 46 346 70 HOH HOH . J 7 HOH A 47 347 7 HOH HOH . J 7 HOH A 48 348 56 HOH HOH . J 7 HOH A 49 349 39 HOH HOH . J 7 HOH A 50 350 27 HOH HOH . J 7 HOH A 51 351 87 HOH HOH . J 7 HOH A 52 352 40 HOH HOH . J 7 HOH A 53 353 75 HOH HOH . J 7 HOH A 54 354 61 HOH HOH . J 7 HOH A 55 355 12 HOH HOH . J 7 HOH A 56 356 9 HOH HOH . J 7 HOH A 57 357 5 HOH HOH . J 7 HOH A 58 358 43 HOH HOH . J 7 HOH A 59 359 47 HOH HOH . J 7 HOH A 60 360 15 HOH HOH . J 7 HOH A 61 361 68 HOH HOH . J 7 HOH A 62 362 78 HOH HOH . J 7 HOH A 63 363 19 HOH HOH . J 7 HOH A 64 364 88 HOH HOH . J 7 HOH A 65 365 52 HOH HOH . J 7 HOH A 66 366 71 HOH HOH . J 7 HOH A 67 367 21 HOH HOH . J 7 HOH A 68 368 17 HOH HOH . J 7 HOH A 69 369 29 HOH HOH . J 7 HOH A 70 370 25 HOH HOH . J 7 HOH A 71 371 51 HOH HOH . J 7 HOH A 72 372 57 HOH HOH . J 7 HOH A 73 373 83 HOH HOH . J 7 HOH A 74 374 14 HOH HOH . J 7 HOH A 75 375 84 HOH HOH . J 7 HOH A 76 376 64 HOH HOH . J 7 HOH A 77 377 22 HOH HOH . J 7 HOH A 78 378 86 HOH HOH . J 7 HOH A 79 379 89 HOH HOH . J 7 HOH A 80 380 90 HOH HOH . J 7 HOH A 81 381 62 HOH HOH . J 7 HOH A 82 382 37 HOH HOH . J 7 HOH A 83 383 1 HOH HOH . J 7 HOH A 84 384 85 HOH HOH . J 7 HOH A 85 385 73 HOH HOH . J 7 HOH A 86 386 79 HOH HOH . J 7 HOH A 87 387 74 HOH HOH . J 7 HOH A 88 388 42 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 P PG APC . . . C 3 -2.75 -5.277 -3.771 1 10.46 ? PG APC 202 A 1 HETATM 2 O O1G APC . . . C 3 -3.232 -5.364 -5.168 1 13.86 ? O1G APC 202 A 1 HETATM 3 O O2G APC . . . C 3 -1.987 -6.408 -3.191 1 12.81 ? O2G APC 202 A 1 HETATM 4 O O3G APC . . . C 3 -2.095 -3.933 -3.493 1 10.36 ? O3G APC 202 A 1 HETATM 5 P PB APC . . . C 3 -5.25 -6.301 -2.691 1 11.12 ? PB APC 202 A 1 HETATM 6 O O1B APC . . . C 3 -4.788 -7.625 -3.18 1 9.95 ? O1B APC 202 A 1 HETATM 7 O O2B APC . . . C 3 -5.767 -6.209 -1.306 1 11.87 ? O2B APC 202 A 1 HETATM 8 O O3B APC . . . C 3 -4.03 -5.248 -2.853 1 10.83 ? O3B APC 202 A 1 HETATM 9 P PA APC . . . C 3 -8.026 -6.638 -3.934 1 10.17 ? PA APC 202 A 1 HETATM 10 O O1A APC . . . C 3 -7.661 -8.049 -3.59 1 8.81 ? O1A APC 202 A 1 HETATM 11 O O2A APC . . . C 3 -9.003 -5.991 -2.994 1 11.73 ? O2A APC 202 A 1 HETATM 12 C C3A APC . . . C 3 -6.445 -5.692 -3.848 1 9.96 ? C3A APC 202 A 1 HETATM 13 O O5' APC . . . C 3 -8.49 -6.733 -5.459 1 10.58 ? O5' APC 202 A 1 HETATM 14 C C5' APC . . . C 3 -9.122 -5.648 -6.108 1 11.27 ? C5' APC 202 A 1 HETATM 15 C C4' APC . . . C 3 -9.242 -5.963 -7.594 1 10.86 ? C4' APC 202 A 1 HETATM 16 O O4' APC . . . C 3 -7.952 -6.206 -8.237 1 10.11 ? O4' APC 202 A 1 HETATM 17 C C3' APC . . . C 3 -9.867 -7.248 -8.025 1 11.07 ? C3' APC 202 A 1 HETATM 18 O O3' APC . . . C 3 -11.302 -7.223 -7.936 1 12.19 ? O3' APC 202 A 1 HETATM 19 C C2' APC . . . C 3 -9.336 -7.538 -9.415 1 10.11 ? C2' APC 202 A 1 HETATM 20 O O2' APC . . . C 3 -10.284 -7.096 -10.359 1 10.19 ? O2' APC 202 A 1 HETATM 21 C C1' APC . . . C 3 -8.193 -6.56 -9.577 1 9.85 ? C1' APC 202 A 1 HETATM 22 N N9 APC . . . C 3 -6.942 -7.02 -10.11 1 9.1 ? N9 APC 202 A 1 HETATM 23 C C8 APC . . . C 3 -6.164 -6.3 -10.951 1 8.43 ? C8 APC 202 A 1 HETATM 24 N N7 APC . . . C 3 -4.992 -6.886 -11.222 1 8.77 ? N7 APC 202 A 1 HETATM 25 C C5 APC . . . C 3 -5.047 -8.088 -10.521 1 7.56 ? C5 APC 202 A 1 HETATM 26 C C6 APC . . . C 3 -4.119 -9.122 -10.417 1 7.34 ? C6 APC 202 A 1 HETATM 27 N N6 APC . . . C 3 -2.923 -9.065 -11.044 1 7.41 ? N6 APC 202 A 1 HETATM 28 N N1 APC . . . C 3 -4.426 -10.168 -9.621 1 6.67 ? N1 APC 202 A 1 HETATM 29 C C2 APC . . . C 3 -5.617 -10.156 -9.033 1 7.49 ? C2 APC 202 A 1 HETATM 30 N N3 APC . . . C 3 -6.564 -9.193 -9.023 1 7.56 ? N3 APC 202 A 1 HETATM 31 C C4 APC . . . C 3 -6.223 -8.157 -9.787 1 8.27 ? C4 APC 202 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 304 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 31 #