data_5XR6 # _model_server_result.job_id 8Hje91yVWC11-DLb3RZfIQ _model_server_result.datetime_utc '2024-10-10 07:18:51' _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 5xr6 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":301}' # _entry.id 5XR6 # _exptl.entry_id 5XR6 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _entity.pdbx_number_of_molecules 2 _entity.pdbx_parent_entity_id . _entity.pdbx_mutation ? _entity.pdbx_fragment ? _entity.pdbx_ec ? # _cell.angle_alpha 88.53 _cell.angle_beta 74.15 _cell.angle_gamma 84.37 _cell.entry_id 5XR6 _cell.length_a 37.634 _cell.length_b 48.416 _cell.length_c 68.508 _cell.Z_PDB 2 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5XR6 _symmetry.cell_setting ? _symmetry.Int_Tables_number 1 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 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 monomeric 1 author_and_software_defined_assembly 1 PISA monomeric 1 author_and_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,C,D,G 1 1 B,E,F,H 2 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 # 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 OG SER 39 A SER 27 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.999 ? metalc ? metalc2 A OG1 THR 57 A THR 45 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.344 ? metalc ? metalc3 C O2G GNP . A GNP 301 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc4 C O2B GNP . A GNP 301 1_555 D MG MG . A MG 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.39 ? metalc ? metalc5 B OG SER 39 B SER 27 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.448 ? metalc ? metalc6 B OG1 THR 57 B THR 45 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.258 ? metalc ? metalc7 E O1G GNP . B GNP 201 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.918 ? metalc ? metalc8 E O1B GNP . B GNP 201 1_555 F MG MG . B MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.099 ? metalc ? metalc9 F MG MG . B MG 202 1_555 H O HOH . B HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.057 ? # _chem_comp.formula 'C10 H17 N6 O13 P3' _chem_comp.formula_weight 522.196 _chem_comp.id GNP _chem_comp.mon_nstd_flag . _chem_comp.name 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE ESTER' _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 PG O1G GNP doub 129 n n PG O2G GNP sing 130 n n PG O3G GNP sing 131 n n PG N3B GNP sing 132 n n O2G HOG2 GNP sing 133 n n O3G HOG3 GNP sing 134 n n N3B PB GNP sing 135 n n N3B HNB3 GNP sing 136 n n PB O1B GNP doub 137 n n PB O2B GNP sing 138 n n PB O3A GNP sing 139 n n O2B HOB2 GNP sing 140 n n O3A PA GNP sing 141 n n PA O1A GNP doub 142 n n PA O2A GNP sing 143 n n PA O5' GNP sing 144 n n O2A HOA2 GNP sing 145 n n O5' C5' GNP sing 146 n n C5' C4' GNP sing 147 n n C5' "H5'2" GNP sing 148 n n C5' "H5'1" GNP sing 149 n n C4' O4' GNP sing 150 n n C4' C3' GNP sing 151 n n C4' H4' GNP sing 152 n n O4' C1' GNP sing 153 n n C3' O3' GNP sing 154 n n C3' C2' GNP sing 155 n n C3' H3' GNP sing 156 n n O3' HO3' GNP sing 157 n n C2' O2' GNP sing 158 n n C2' C1' GNP sing 159 n n C2' H2' GNP sing 160 n n O2' HO2' GNP sing 161 n n C1' N9 GNP sing 162 n n C1' H1' GNP sing 163 n n N9 C8 GNP sing 164 n y N9 C4 GNP sing 165 n y C8 N7 GNP doub 166 n y C8 H8 GNP sing 167 n n N7 C5 GNP sing 168 n y C5 C6 GNP sing 169 n y C5 C4 GNP doub 170 n y C6 O6 GNP doub 171 n n C6 N1 GNP sing 172 n y N1 C2 GNP sing 173 n y N1 HN1 GNP sing 174 n n C2 N2 GNP sing 175 n n C2 N3 GNP doub 176 n y N2 HN21 GNP sing 177 n n N2 HN22 GNP sing 178 n n N3 C4 GNP sing 179 n y # _atom_sites.entry_id 5XR6 _atom_sites.fract_transf_matrix[1][1] 0.026572 _atom_sites.fract_transf_matrix[1][2] -0.002618 _atom_sites.fract_transf_matrix[1][3] -0.007549 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.020754 _atom_sites.fract_transf_matrix[2][3] 0.000026 _atom_sites.fract_transf_matrix[3][1] 0 _atom_sites.fract_transf_matrix[3][2] 0 _atom_sites.fract_transf_matrix[3][3] 0.015174 _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 GNP A 1 301 301 GNP GNP . D 3 MG A 1 302 2 MG MG . E 2 GNP B 1 201 302 GNP GNP . F 3 MG B 1 202 1 MG MG . G 4 HOH A 1 401 17 HOH HOH . G 4 HOH A 2 402 2 HOH HOH . G 4 HOH A 3 403 10 HOH HOH . G 4 HOH A 4 404 22 HOH HOH . G 4 HOH A 5 405 30 HOH HOH . G 4 HOH A 6 406 12 HOH HOH . G 4 HOH A 7 407 40 HOH HOH . G 4 HOH A 8 408 13 HOH HOH . G 4 HOH A 9 409 23 HOH HOH . G 4 HOH A 10 410 33 HOH HOH . G 4 HOH A 11 411 8 HOH HOH . G 4 HOH A 12 412 20 HOH HOH . G 4 HOH A 13 413 21 HOH HOH . G 4 HOH A 14 414 1 HOH HOH . G 4 HOH A 15 415 39 HOH HOH . G 4 HOH A 16 416 29 HOH HOH . G 4 HOH A 17 417 28 HOH HOH . G 4 HOH A 18 418 4 HOH HOH . G 4 HOH A 19 419 37 HOH HOH . G 4 HOH A 20 420 7 HOH HOH . G 4 HOH A 21 421 24 HOH HOH . G 4 HOH A 22 422 18 HOH HOH . G 4 HOH A 23 423 34 HOH HOH . H 4 HOH B 1 301 15 HOH HOH . H 4 HOH B 2 302 11 HOH HOH . H 4 HOH B 3 303 6 HOH HOH . H 4 HOH B 4 304 5 HOH HOH . H 4 HOH B 5 305 16 HOH HOH . H 4 HOH B 6 306 31 HOH HOH . H 4 HOH B 7 307 38 HOH HOH . H 4 HOH B 8 308 25 HOH HOH . H 4 HOH B 9 309 19 HOH HOH . H 4 HOH B 10 310 3 HOH HOH . H 4 HOH B 11 311 27 HOH HOH . H 4 HOH B 12 312 41 HOH HOH . H 4 HOH B 13 313 14 HOH HOH . H 4 HOH B 14 314 32 HOH HOH . H 4 HOH B 15 315 35 HOH HOH . H 4 HOH B 16 316 26 HOH HOH . H 4 HOH B 17 317 9 HOH HOH . H 4 HOH B 18 318 36 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 GNP . . . C 2 -120.517 50.093 15.645 1 32.57 ? PG GNP 301 A 1 HETATM 2 O O1G GNP . . . C 2 -119.218 50.526 15.006 1 42.11 ? O1G GNP 301 A 1 HETATM 3 O O2G GNP . . . C 2 -120.399 49.157 16.824 1 38.63 ? O2G GNP 301 A 1 HETATM 4 O O3G GNP . . . C 2 -121.127 51.457 15.882 1 33.64 ? O3G GNP 301 A 1 HETATM 5 N N3B GNP . . . C 2 -121.343 49.234 14.595 1 34.82 ? N3B GNP 301 A 1 HETATM 6 P PB GNP . . . C 2 -121.123 47.723 14.124 1 29.56 ? PB GNP 301 A 1 HETATM 7 O O1B GNP . . . C 2 -120.194 47.753 12.963 1 36.54 ? O1B GNP 301 A 1 HETATM 8 O O2B GNP . . . C 2 -120.792 46.777 15.21 1 29.99 ? O2B GNP 301 A 1 HETATM 9 O O3A GNP . . . C 2 -122.506 47.282 13.623 1 39.7 ? O3A GNP 301 A 1 HETATM 10 P PA GNP . . . C 2 -123.361 46.151 14.223 1 34.75 ? PA GNP 301 A 1 HETATM 11 O O1A GNP . . . C 2 -122.581 44.884 14.234 1 34.11 ? O1A GNP 301 A 1 HETATM 12 O O2A GNP . . . C 2 -123.991 46.591 15.496 1 41.05 ? O2A GNP 301 A 1 HETATM 13 O O5' GNP . . . C 2 -124.549 45.963 13.209 1 41.9 ? O5' GNP 301 A 1 HETATM 14 C C5' GNP . . . C 2 -125.072 47.135 12.579 1 42.34 ? C5' GNP 301 A 1 HETATM 15 C C4' GNP . . . C 2 -126.398 46.853 11.891 1 42.5 ? C4' GNP 301 A 1 HETATM 16 O O4' GNP . . . C 2 -126.165 46.189 10.624 1 41.6 ? O4' GNP 301 A 1 HETATM 17 C C3' GNP . . . C 2 -127.349 45.977 12.7 1 45.41 ? C3' GNP 301 A 1 HETATM 18 O O3' GNP . . . C 2 -128.631 46.595 12.708 1 54.69 ? O3' GNP 301 A 1 HETATM 19 C C2' GNP . . . C 2 -127.344 44.631 11.974 1 45.72 ? C2' GNP 301 A 1 HETATM 20 O O2' GNP . . . C 2 -128.614 44.046 11.841 1 47.67 ? O2' GNP 301 A 1 HETATM 21 C C1' GNP . . . C 2 -126.87 44.965 10.569 1 45.51 ? C1' GNP 301 A 1 HETATM 22 N N9 GNP . . . C 2 -126.043 43.871 10.058 1 43.98 ? N9 GNP 301 A 1 HETATM 23 C C8 GNP . . . C 2 -124.834 43.432 10.536 1 37.51 ? C8 GNP 301 A 1 HETATM 24 N N7 GNP . . . C 2 -124.357 42.406 9.888 1 34.6 ? N7 GNP 301 A 1 HETATM 25 C C5 GNP . . . C 2 -125.311 42.142 8.914 1 42.64 ? C5 GNP 301 A 1 HETATM 26 C C6 GNP . . . C 2 -125.349 41.154 7.902 1 42 ? C6 GNP 301 A 1 HETATM 27 O O6 GNP . . . C 2 -124.533 40.272 7.624 1 40.67 ? O6 GNP 301 A 1 HETATM 28 N N1 GNP . . . C 2 -126.508 41.25 7.157 1 43.73 ? N1 GNP 301 A 1 HETATM 29 C C2 GNP . . . C 2 -127.501 42.169 7.346 1 41.08 ? C2 GNP 301 A 1 HETATM 30 N N2 GNP . . . C 2 -128.53 42.086 6.498 1 42.76 ? N2 GNP 301 A 1 HETATM 31 N N3 GNP . . . C 2 -127.484 43.108 8.27 1 38.2 ? N3 GNP 301 A 1 HETATM 32 C C4 GNP . . . C 2 -126.361 43.033 9.013 1 42.37 ? C4 GNP 301 A 1 # _model_server_stats.io_time_ms 61 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 263 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #