data_1G3R # _model_server_result.job_id D1uGRsHoh1CTRUs1zpfFdw _model_server_result.datetime_utc '2025-03-05 02:42:58' _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 1g3r # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":238}' # _entry.id 1G3R # _exptl.entry_id 1G3R _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 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE 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 90 _cell.angle_gamma 90 _cell.entry_id 1G3R _cell.length_a 98.644 _cell.length_b 98.644 _cell.length_c 98.644 _cell.Z_PDB 12 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1G3R _symmetry.cell_setting cubic _symmetry.Int_Tables_number 198 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 3' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 OG1 THR 17 A THR 17 1_555 B MG MG . A MG 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.261 ? metalc ? metalc2 C O3G ACP . A ACP 238 1_555 B MG MG . A MG 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.269 ? metalc ? metalc3 C O2B ACP . A ACP 238 1_555 B MG MG . A MG 239 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.531 ? metalc ? metalc4 B MG MG . A MG 239 1_555 D O HOH . A HOH 296 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.473 ? metalc ? metalc5 B MG MG . A MG 239 1_555 D O HOH . A HOH 297 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.56 ? metalc ? metalc6 B MG MG . A MG 239 1_555 D O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.628 ? # _chem_comp.formula 'C11 H18 N5 O12 P3' _chem_comp.formula_weight 505.208 _chem_comp.id ACP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOMETHYLPHOSPHONIC ACID ADENYLATE ESTER' _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ADENOSINE-5'-[BETA, GAMMA-METHYLENE]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 ACP doub 1 n n PG O2G ACP sing 2 n n PG O3G ACP sing 3 n n PG C3B ACP sing 4 n n O2G HOG2 ACP sing 5 n n O3G HOG3 ACP sing 6 n n PB O1B ACP doub 7 n n PB O2B ACP sing 8 n n PB C3B ACP sing 9 n n PB O3A ACP sing 10 n n O2B HOB2 ACP sing 11 n n C3B H3B1 ACP sing 12 n n C3B H3B2 ACP sing 13 n n PA O1A ACP doub 14 n n PA O2A ACP sing 15 n n PA O3A ACP sing 16 n n PA O5' ACP sing 17 n n O2A HOA2 ACP sing 18 n n O5' C5' ACP sing 19 n n C5' C4' ACP sing 20 n n C5' "H5'1" ACP sing 21 n n C5' "H5'2" ACP sing 22 n n C4' O4' ACP sing 23 n n C4' C3' ACP sing 24 n n C4' H4' ACP sing 25 n n O4' C1' ACP sing 26 n n C3' O3' ACP sing 27 n n C3' C2' ACP sing 28 n n C3' H3' ACP sing 29 n n O3' HO3' ACP sing 30 n n C2' O2' ACP sing 31 n n C2' C1' ACP sing 32 n n C2' H2' ACP sing 33 n n O2' HO2' ACP sing 34 n n C1' N9 ACP sing 35 n n C1' H1' ACP sing 36 n n N9 C8 ACP sing 37 n y N9 C4 ACP sing 38 n y C8 N7 ACP doub 39 n y C8 H8 ACP sing 40 n n N7 C5 ACP sing 41 n y C5 C6 ACP sing 42 n y C5 C4 ACP doub 43 n y C6 N6 ACP sing 44 n n C6 N1 ACP doub 45 n y N6 HN61 ACP sing 46 n n N6 HN62 ACP sing 47 n n N1 C2 ACP sing 48 n y C2 N3 ACP doub 49 n y C2 H2 ACP sing 50 n n N3 C4 ACP sing 51 n y # _atom_sites.entry_id 1G3R _atom_sites.fract_transf_matrix[1][1] 0.010137 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010137 _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] 0.010137 _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 MG A 1 239 239 MG MG . C 3 ACP A 1 238 238 ACP ACP . D 4 HOH A 1 240 1 HOH HOH . D 4 HOH A 2 241 2 HOH HOH . D 4 HOH A 3 242 3 HOH HOH . D 4 HOH A 4 243 4 HOH HOH . D 4 HOH A 5 244 5 HOH HOH . D 4 HOH A 6 245 6 HOH HOH . D 4 HOH A 7 246 7 HOH HOH . D 4 HOH A 8 247 8 HOH HOH . D 4 HOH A 9 248 9 HOH HOH . D 4 HOH A 10 249 10 HOH HOH . D 4 HOH A 11 250 11 HOH HOH . D 4 HOH A 12 251 12 HOH HOH . D 4 HOH A 13 252 13 HOH HOH . D 4 HOH A 14 253 14 HOH HOH . D 4 HOH A 15 254 15 HOH HOH . D 4 HOH A 16 255 16 HOH HOH . D 4 HOH A 17 256 17 HOH HOH . D 4 HOH A 18 257 18 HOH HOH . D 4 HOH A 19 258 19 HOH HOH . D 4 HOH A 20 259 20 HOH HOH . D 4 HOH A 21 260 21 HOH HOH . D 4 HOH A 22 261 22 HOH HOH . D 4 HOH A 23 262 24 HOH HOH . D 4 HOH A 24 263 25 HOH HOH . D 4 HOH A 25 264 26 HOH HOH . D 4 HOH A 26 265 27 HOH HOH . D 4 HOH A 27 266 28 HOH HOH . D 4 HOH A 28 267 29 HOH HOH . D 4 HOH A 29 268 30 HOH HOH . D 4 HOH A 30 269 31 HOH HOH . D 4 HOH A 31 270 32 HOH HOH . D 4 HOH A 32 271 33 HOH HOH . D 4 HOH A 33 272 34 HOH HOH . D 4 HOH A 34 273 35 HOH HOH . D 4 HOH A 35 274 36 HOH HOH . D 4 HOH A 36 275 37 HOH HOH . D 4 HOH A 37 276 38 HOH HOH . D 4 HOH A 38 277 39 HOH HOH . D 4 HOH A 39 278 40 HOH HOH . D 4 HOH A 40 279 41 HOH HOH . D 4 HOH A 41 280 42 HOH HOH . D 4 HOH A 42 281 43 HOH HOH . D 4 HOH A 43 282 44 HOH HOH . D 4 HOH A 44 283 45 HOH HOH . D 4 HOH A 45 284 46 HOH HOH . D 4 HOH A 46 285 47 HOH HOH . D 4 HOH A 47 286 48 HOH HOH . D 4 HOH A 48 287 49 HOH HOH . D 4 HOH A 49 288 50 HOH HOH . D 4 HOH A 50 289 51 HOH HOH . D 4 HOH A 51 290 52 HOH HOH . D 4 HOH A 52 291 53 HOH HOH . D 4 HOH A 53 292 54 HOH HOH . D 4 HOH A 54 293 55 HOH HOH . D 4 HOH A 55 294 56 HOH HOH . D 4 HOH A 56 295 57 HOH HOH . D 4 HOH A 57 296 58 HOH HOH . D 4 HOH A 58 297 59 HOH HOH . D 4 HOH A 59 298 60 HOH HOH . D 4 HOH A 60 299 61 HOH HOH . D 4 HOH A 61 300 62 HOH HOH . D 4 HOH A 62 301 63 HOH HOH . D 4 HOH A 63 302 64 HOH HOH . D 4 HOH A 64 303 65 HOH HOH . D 4 HOH A 65 304 66 HOH HOH . D 4 HOH A 66 305 67 HOH HOH . D 4 HOH A 67 306 68 HOH HOH . D 4 HOH A 68 307 69 HOH HOH . D 4 HOH A 69 308 70 HOH HOH . D 4 HOH A 70 309 71 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 ACP . . . C 3 83.571 -12.813 126.817 1 51.83 ? PG ACP 238 A 1 HETATM 2 O O1G ACP . . . C 3 82.323 -12.949 126.192 1 52.61 ? O1G ACP 238 A 1 HETATM 3 O O2G ACP . . . C 3 84.488 -13.876 126.448 1 51.97 ? O2G ACP 238 A 1 HETATM 4 O O3G ACP . . . C 3 83.262 -13.029 128.291 1 52.43 ? O3G ACP 238 A 1 HETATM 5 P PB ACP . . . C 3 83.735 -9.925 127.597 1 49.21 ? PB ACP 238 A 1 HETATM 6 O O1B ACP . . . C 3 82.383 -9.49 127.38 1 48.56 ? O1B ACP 238 A 1 HETATM 7 O O2B ACP . . . C 3 83.986 -10.075 129.044 1 49.06 ? O2B ACP 238 A 1 HETATM 8 C C3B ACP . . . C 3 84.203 -11.332 126.785 1 50.13 ? C3B ACP 238 A 1 HETATM 9 P PA ACP . . . C 3 85.841 -8.044 127.759 1 46.93 ? PA ACP 238 A 1 HETATM 10 O O1A ACP . . . C 3 86.975 -8.819 128.107 1 46.06 ? O1A ACP 238 A 1 HETATM 11 O O2A ACP . . . C 3 85.329 -7.233 128.841 1 46 ? O2A ACP 238 A 1 HETATM 12 O O3A ACP . . . C 3 84.707 -8.819 127.131 1 48.47 ? O3A ACP 238 A 1 HETATM 13 O O5' ACP . . . C 3 86.31 -7.118 126.677 1 46.98 ? O5' ACP 238 A 1 HETATM 14 C C5' ACP . . . C 3 86.914 -7.541 125.41 1 47.3 ? C5' ACP 238 A 1 HETATM 15 C C4' ACP . . . C 3 88.069 -6.675 125.067 1 47.53 ? C4' ACP 238 A 1 HETATM 16 O O4' ACP . . . C 3 87.63 -5.358 124.62 1 47.09 ? O4' ACP 238 A 1 HETATM 17 C C3' ACP . . . C 3 89.005 -6.388 126.208 1 47.53 ? C3' ACP 238 A 1 HETATM 18 O O3' ACP . . . C 3 90.369 -6.532 125.807 1 48.86 ? O3' ACP 238 A 1 HETATM 19 C C2' ACP . . . C 3 88.744 -4.98 126.628 1 47.03 ? C2' ACP 238 A 1 HETATM 20 O O2' ACP . . . C 3 89.858 -4.274 127.15 1 47.72 ? O2' ACP 238 A 1 HETATM 21 C C1' ACP . . . C 3 88.235 -4.312 125.419 1 47.16 ? C1' ACP 238 A 1 HETATM 22 N N9 ACP . . . C 3 87.137 -3.339 125.668 1 46.75 ? N9 ACP 238 A 1 HETATM 23 C C8 ACP . . . C 3 85.899 -3.457 126.311 1 46.15 ? C8 ACP 238 A 1 HETATM 24 N N7 ACP . . . C 3 85.179 -2.374 126.344 1 46.77 ? N7 ACP 238 A 1 HETATM 25 C C5 ACP . . . C 3 85.963 -1.448 125.683 1 46.72 ? C5 ACP 238 A 1 HETATM 26 C C6 ACP . . . C 3 85.77 -0.067 125.368 1 46.61 ? C6 ACP 238 A 1 HETATM 27 N N6 ACP . . . C 3 84.649 0.547 125.739 1 46.73 ? N6 ACP 238 A 1 HETATM 28 N N1 ACP . . . C 3 86.778 0.605 124.671 1 46.5 ? N1 ACP 238 A 1 HETATM 29 C C2 ACP . . . C 3 87.918 -0.045 124.3 1 46.79 ? C2 ACP 238 A 1 HETATM 30 N N3 ACP . . . C 3 88.179 -1.353 124.559 1 46.43 ? N3 ACP 238 A 1 HETATM 31 C C4 ACP . . . C 3 87.165 -2.004 125.255 1 46.43 ? C4 ACP 238 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 320 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 31 #