data_5WPM # _model_server_result.job_id '_saF3m3OFot3jXLjg8pCuQ' _model_server_result.datetime_utc '2024-11-02 04:36:41' _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 5wpm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":201}' # _entry.id 5WPM # _exptl.entry_id 5WPM _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 'PHOSPHOAMINOPHOSPHONIC ACID-GUANYLATE 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 103.38 _cell.angle_gamma 90 _cell.entry_id 5WPM _cell.length_a 41.934 _cell.length_b 37.81 _cell.length_c 70.179 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5WPM _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 trimeric _pdbx_struct_assembly.oligomeric_count 3 _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 D _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 disulf ? disulf1 B SG CYS 7 B CYS 7 1_555 C SG CYS 7 C CYS 7 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc1 A OG SER 17 A SER 17 1_555 E MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.196 ? metalc ? metalc2 A O VAL 81 A VAL 81 1_555 F MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.845 ? metalc ? metalc3 A O SER 89 A SER 89 1_555 F MG MG . A MG 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.45 ? metalc ? metalc4 D O2G GNP . A GNP 201 1_555 E MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.984 ? metalc ? metalc5 D O2B GNP . A GNP 201 1_555 E MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.059 ? metalc ? metalc6 E MG MG . A MG 202 1_555 H O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.132 ? metalc ? metalc7 E MG MG . A MG 202 1_555 H O HOH . A HOH 314 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.968 ? metalc ? metalc8 E MG MG . A MG 202 1_555 H O HOH . A HOH 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.014 ? # _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 5WPM _atom_sites.fract_transf_matrix[1][1] 0.023847 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.00567 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.026448 _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] 0.014647 _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 D 3 GNP A 1 201 180 GNP GNP . E 4 MG A 1 202 181 MG MG . F 4 MG A 1 203 1 MG MG . G 5 SO4 C 1 101 2 SO4 SO4 . H 6 HOH A 1 301 55 HOH HOH . H 6 HOH A 2 302 65 HOH HOH . H 6 HOH A 3 303 8 HOH HOH . H 6 HOH A 4 304 26 HOH HOH . H 6 HOH A 5 305 30 HOH HOH . H 6 HOH A 6 306 9 HOH HOH . H 6 HOH A 7 307 35 HOH HOH . H 6 HOH A 8 308 36 HOH HOH . H 6 HOH A 9 309 7 HOH HOH . H 6 HOH A 10 310 45 HOH HOH . H 6 HOH A 11 311 75 HOH HOH . H 6 HOH A 12 312 14 HOH HOH . H 6 HOH A 13 313 25 HOH HOH . H 6 HOH A 14 314 5 HOH HOH . H 6 HOH A 15 315 3 HOH HOH . H 6 HOH A 16 316 1 HOH HOH . H 6 HOH A 17 317 6 HOH HOH . H 6 HOH A 18 318 33 HOH HOH . H 6 HOH A 19 319 34 HOH HOH . H 6 HOH A 20 320 37 HOH HOH . H 6 HOH A 21 321 46 HOH HOH . H 6 HOH A 22 322 24 HOH HOH . H 6 HOH A 23 323 71 HOH HOH . H 6 HOH A 24 324 31 HOH HOH . H 6 HOH A 25 325 28 HOH HOH . H 6 HOH A 26 326 27 HOH HOH . H 6 HOH A 27 327 69 HOH HOH . H 6 HOH A 28 328 43 HOH HOH . H 6 HOH A 29 329 50 HOH HOH . H 6 HOH A 30 330 11 HOH HOH . H 6 HOH A 31 331 32 HOH HOH . I 6 HOH B 1 101 15 HOH HOH . I 6 HOH B 2 102 51 HOH HOH . I 6 HOH B 3 103 12 HOH HOH . I 6 HOH B 4 104 38 HOH HOH . I 6 HOH B 5 105 39 HOH HOH . I 6 HOH B 6 106 17 HOH HOH . I 6 HOH B 7 107 2 HOH HOH . I 6 HOH B 8 108 47 HOH HOH . I 6 HOH B 9 109 18 HOH HOH . I 6 HOH B 10 110 10 HOH HOH . I 6 HOH B 11 111 57 HOH HOH . I 6 HOH B 12 112 40 HOH HOH . I 6 HOH B 13 113 58 HOH HOH . I 6 HOH B 14 114 20 HOH HOH . I 6 HOH B 15 115 59 HOH HOH . I 6 HOH B 16 116 52 HOH HOH . I 6 HOH B 17 117 53 HOH HOH . I 6 HOH B 18 118 56 HOH HOH . I 6 HOH B 19 119 16 HOH HOH . I 6 HOH B 20 120 42 HOH HOH . J 6 HOH C 1 201 19 HOH HOH . J 6 HOH C 2 202 66 HOH HOH . J 6 HOH C 3 203 63 HOH HOH . J 6 HOH C 4 204 60 HOH HOH . J 6 HOH C 5 205 41 HOH HOH . J 6 HOH C 6 206 48 HOH HOH . J 6 HOH C 7 207 21 HOH HOH . J 6 HOH C 8 208 49 HOH HOH . J 6 HOH C 9 209 54 HOH HOH . J 6 HOH C 10 210 61 HOH HOH . J 6 HOH C 11 211 22 HOH HOH . J 6 HOH C 12 212 67 HOH HOH . J 6 HOH C 13 213 72 HOH HOH . J 6 HOH C 14 214 73 HOH HOH . J 6 HOH C 15 215 62 HOH HOH . J 6 HOH C 16 216 64 HOH HOH . J 6 HOH C 17 217 74 HOH HOH . J 6 HOH C 18 218 68 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 . . . D 3 81.123 -49.294 19.081 1 24.87 ? PG GNP 201 A 1 HETATM 2 O O1G GNP . . . D 3 79.635 -48.755 19.317 1 22 ? O1G GNP 201 A 1 HETATM 3 O O2G GNP . . . D 3 82.237 -48.234 19.542 1 25.47 ? O2G GNP 201 A 1 HETATM 4 O O3G GNP . . . D 3 81.314 -50.565 19.829 1 25.72 ? O3G GNP 201 A 1 HETATM 5 N N3B GNP . . . D 3 81.366 -49.614 17.396 1 25.03 ? N3B GNP 201 A 1 HETATM 6 P PB GNP . . . D 3 81.237 -48.326 16.23 1 25.27 ? PB GNP 201 A 1 HETATM 7 O O1B GNP . . . D 3 79.832 -47.907 16.033 1 21.49 ? O1B GNP 201 A 1 HETATM 8 O O2B GNP . . . D 3 82.148 -47.078 16.661 1 26.89 ? O2B GNP 201 A 1 HETATM 9 O O3A GNP . . . D 3 81.707 -48.978 14.838 1 24.12 ? O3A GNP 201 A 1 HETATM 10 P PA GNP . . . D 3 83.228 -49.023 14.36 1 26.72 ? PA GNP 201 A 1 HETATM 11 O O1A GNP . . . D 3 83.535 -47.675 13.748 1 28.87 ? O1A GNP 201 A 1 HETATM 12 O O2A GNP . . . D 3 84.105 -49.592 15.441 1 26.42 ? O2A GNP 201 A 1 HETATM 13 O O5' GNP . . . D 3 83.124 -50.126 13.197 1 27.62 ? O5' GNP 201 A 1 HETATM 14 C C5' GNP . . . D 3 82.851 -51.502 13.497 1 27.34 ? C5' GNP 201 A 1 HETATM 15 C C4' GNP . . . D 3 83.271 -52.366 12.325 1 33.09 ? C4' GNP 201 A 1 HETATM 16 O O4' GNP . . . D 3 82.547 -51.944 11.172 1 30.63 ? O4' GNP 201 A 1 HETATM 17 C C3' GNP . . . D 3 84.747 -52.217 11.991 1 31.14 ? C3' GNP 201 A 1 HETATM 18 O O3' GNP . . . D 3 85.289 -53.48 11.586 1 34.76 ? O3' GNP 201 A 1 HETATM 19 C C2' GNP . . . D 3 84.778 -51.257 10.825 1 31.87 ? C2' GNP 201 A 1 HETATM 20 O O2' GNP . . . D 3 85.902 -51.461 9.971 1 32.76 ? O2' GNP 201 A 1 HETATM 21 C C1' GNP . . . D 3 83.463 -51.58 10.141 1 31.18 ? C1' GNP 201 A 1 HETATM 22 N N9 GNP . . . D 3 82.91 -50.444 9.385 1 32.34 ? N9 GNP 201 A 1 HETATM 23 C C8 GNP . . . D 3 82.594 -49.231 9.879 1 32.55 ? C8 GNP 201 A 1 HETATM 24 N N7 GNP . . . D 3 82.103 -48.434 8.899 1 29.19 ? N7 GNP 201 A 1 HETATM 25 C C5 GNP . . . D 3 82.109 -49.149 7.761 1 32.6 ? C5 GNP 201 A 1 HETATM 26 C C6 GNP . . . D 3 81.727 -48.929 6.349 1 33.92 ? C6 GNP 201 A 1 HETATM 27 O O6 GNP . . . D 3 81.261 -47.838 5.977 1 32.89 ? O6 GNP 201 A 1 HETATM 28 N N1 GNP . . . D 3 81.882 -49.94 5.478 1 35.19 ? N1 GNP 201 A 1 HETATM 29 C C2 GNP . . . D 3 82.38 -51.145 5.837 1 35.53 ? C2 GNP 201 A 1 HETATM 30 N N2 GNP . . . D 3 82.515 -52.123 4.903 1 37.32 ? N2 GNP 201 A 1 HETATM 31 N N3 GNP . . . D 3 82.752 -51.418 7.116 1 32.94 ? N3 GNP 201 A 1 HETATM 32 C C4 GNP . . . D 3 82.636 -50.479 8.092 1 32.19 ? C4 GNP 201 A 1 # _model_server_stats.io_time_ms 11 _model_server_stats.parse_time_ms 10 _model_server_stats.create_model_time_ms 10 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #