data_4YC7 # _model_server_result.job_id nsfpdlf1kM832vlPaUXJ7w _model_server_result.datetime_utc '2024-11-22 14:27:37' _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 4yc7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":201}' # _entry.id 4YC7 # _exptl.entry_id 4YC7 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 3 _entity.src_method man _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 90 _cell.angle_gamma 90 _cell.entry_id 4YC7 _cell.length_a 91.094 _cell.length_b 91.094 _cell.length_c 144.275 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4YC7 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _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 B OG1 THR 19 A THR 16 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.812 ? metalc ? metalc2 B O VAL 35 A VAL 32 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.905 ? metalc ? metalc3 C O2G GNP . A GNP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.769 ? metalc ? metalc4 C O2B GNP . A GNP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.678 ? metalc ? metalc5 C O2A GNP . A GNP 201 1_555 D MG MG . A MG 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.899 ? metalc ? metalc6 D MG MG . A MG 202 1_555 F O HOH . A HOH 315 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.839 ? # _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 4YC7 _atom_sites.fract_transf_matrix[1][1] 0.010978 _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] 0.010978 _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] 0.006931 _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 3 GNP A 1 201 179 GNP GNP . D 4 MG A 1 202 180 MG MG . E 5 HOH B 1 401 47 HOH HOH . E 5 HOH B 2 402 4 HOH HOH . E 5 HOH B 3 403 6 HOH HOH . E 5 HOH B 4 404 7 HOH HOH . E 5 HOH B 5 405 12 HOH HOH . E 5 HOH B 6 406 14 HOH HOH . E 5 HOH B 7 407 15 HOH HOH . E 5 HOH B 8 408 16 HOH HOH . E 5 HOH B 9 409 17 HOH HOH . E 5 HOH B 10 410 18 HOH HOH . E 5 HOH B 11 411 19 HOH HOH . E 5 HOH B 12 412 21 HOH HOH . E 5 HOH B 13 413 23 HOH HOH . E 5 HOH B 14 414 24 HOH HOH . E 5 HOH B 15 415 25 HOH HOH . E 5 HOH B 16 416 26 HOH HOH . E 5 HOH B 17 417 32 HOH HOH . E 5 HOH B 18 418 36 HOH HOH . E 5 HOH B 19 419 37 HOH HOH . E 5 HOH B 20 420 39 HOH HOH . E 5 HOH B 21 421 40 HOH HOH . E 5 HOH B 22 422 42 HOH HOH . E 5 HOH B 23 423 43 HOH HOH . E 5 HOH B 24 424 44 HOH HOH . E 5 HOH B 25 425 46 HOH HOH . E 5 HOH B 26 426 51 HOH HOH . E 5 HOH B 27 427 53 HOH HOH . E 5 HOH B 28 428 54 HOH HOH . E 5 HOH B 29 429 55 HOH HOH . E 5 HOH B 30 430 56 HOH HOH . E 5 HOH B 31 431 58 HOH HOH . E 5 HOH B 32 432 59 HOH HOH . E 5 HOH B 33 433 60 HOH HOH . E 5 HOH B 34 434 63 HOH HOH . F 5 HOH A 1 301 57 HOH HOH . F 5 HOH A 2 302 29 HOH HOH . F 5 HOH A 3 303 50 HOH HOH . F 5 HOH A 4 304 1 HOH HOH . F 5 HOH A 5 305 2 HOH HOH . F 5 HOH A 6 306 3 HOH HOH . F 5 HOH A 7 307 5 HOH HOH . F 5 HOH A 8 308 8 HOH HOH . F 5 HOH A 9 309 9 HOH HOH . F 5 HOH A 10 310 10 HOH HOH . F 5 HOH A 11 311 11 HOH HOH . F 5 HOH A 12 312 13 HOH HOH . F 5 HOH A 13 313 20 HOH HOH . F 5 HOH A 14 314 22 HOH HOH . F 5 HOH A 15 315 27 HOH HOH . F 5 HOH A 16 316 28 HOH HOH . F 5 HOH A 17 317 30 HOH HOH . F 5 HOH A 18 318 31 HOH HOH . F 5 HOH A 19 319 33 HOH HOH . F 5 HOH A 20 320 34 HOH HOH . F 5 HOH A 21 321 35 HOH HOH . F 5 HOH A 22 322 38 HOH HOH . F 5 HOH A 23 323 41 HOH HOH . F 5 HOH A 24 324 45 HOH HOH . F 5 HOH A 25 325 48 HOH HOH . F 5 HOH A 26 326 49 HOH HOH . F 5 HOH A 27 327 52 HOH HOH . F 5 HOH A 28 328 61 HOH HOH . F 5 HOH A 29 329 62 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 3 8.208 24.314 -15.407 1 47.3 ? PG GNP 201 A 1 HETATM 2 O O1G GNP . . . C 3 8.039 23.448 -16.661 1 38 ? O1G GNP 201 A 1 HETATM 3 O O2G GNP . . . C 3 7.978 23.464 -14.113 1 38.82 ? O2G GNP 201 A 1 HETATM 4 O O3G GNP . . . C 3 9.493 24.836 -15.429 1 49.93 ? O3G GNP 201 A 1 HETATM 5 N N3B GNP . . . C 3 7.123 25.619 -15.482 1 49.26 ? N3B GNP 201 A 1 HETATM 6 P PB GNP . . . C 3 5.63 25.399 -14.723 1 42.49 ? PB GNP 201 A 1 HETATM 7 O O1B GNP . . . C 3 4.727 25.183 -15.762 1 44.77 ? O1B GNP 201 A 1 HETATM 8 O O2B GNP . . . C 3 5.739 24.161 -13.761 1 32.64 ? O2B GNP 201 A 1 HETATM 9 O O3A GNP . . . C 3 5.17 26.76 -14.154 1 50.96 ? O3A GNP 201 A 1 HETATM 10 P PA GNP . . . C 3 4.802 27.139 -12.706 1 48.5 ? PA GNP 201 A 1 HETATM 11 O O1A GNP . . . C 3 3.679 26.364 -12.277 1 39.71 ? O1A GNP 201 A 1 HETATM 12 O O2A GNP . . . C 3 5.998 27.201 -11.927 1 45.91 ? O2A GNP 201 A 1 HETATM 13 O O5' GNP . . . C 3 4.324 28.592 -12.931 1 53.57 ? O5' GNP 201 A 1 HETATM 14 C C5' GNP . . . C 3 5.245 29.566 -13.33 1 54.75 ? C5' GNP 201 A 1 HETATM 15 C C4' GNP . . . C 3 4.781 30.99 -13.105 1 64.97 ? C4' GNP 201 A 1 HETATM 16 O O4' GNP . . . C 3 3.431 31.182 -13.442 1 66.52 ? O4' GNP 201 A 1 HETATM 17 C C3' GNP . . . C 3 4.858 31.368 -11.663 1 71.31 ? C3' GNP 201 A 1 HETATM 18 O O3' GNP . . . C 3 5.046 32.762 -11.605 1 78.83 ? O3' GNP 201 A 1 HETATM 19 C C2' GNP . . . C 3 3.467 31.253 -11.189 1 76.21 ? C2' GNP 201 A 1 HETATM 20 O O2' GNP . . . C 3 3.38 32.178 -10.133 1 84.56 ? O2' GNP 201 A 1 HETATM 21 C C1' GNP . . . C 3 2.719 31.764 -12.376 1 70.46 ? C1' GNP 201 A 1 HETATM 22 N N9 GNP . . . C 3 1.333 31.263 -12.433 1 70.42 ? N9 GNP 201 A 1 HETATM 23 C C8 GNP . . . C 3 1.013 29.983 -12.445 1 71.21 ? C8 GNP 201 A 1 HETATM 24 N N7 GNP . . . C 3 -0.302 29.806 -12.525 1 67.46 ? N7 GNP 201 A 1 HETATM 25 C C5 GNP . . . C 3 -0.858 31 -12.57 1 70.2 ? C5 GNP 201 A 1 HETATM 26 C C6 GNP . . . C 3 -2.22 31.501 -12.663 1 63.71 ? C6 GNP 201 A 1 HETATM 27 O O6 GNP . . . C 3 -3.17 30.739 -12.716 1 58.11 ? O6 GNP 201 A 1 HETATM 28 N N1 GNP . . . C 3 -2.387 32.796 -12.692 1 60.56 ? N1 GNP 201 A 1 HETATM 29 C C2 GNP . . . C 3 -1.364 33.635 -12.634 1 56.42 ? C2 GNP 201 A 1 HETATM 30 N N2 GNP . . . C 3 -1.634 34.935 -12.663 1 51.6 ? N2 GNP 201 A 1 HETATM 31 N N3 GNP . . . C 3 -0.096 33.257 -12.547 1 51.44 ? N3 GNP 201 A 1 HETATM 32 C C4 GNP . . . C 3 0.22 31.965 -12.512 1 66.09 ? C4 GNP 201 A 1 # _model_server_stats.io_time_ms 32 _model_server_stats.parse_time_ms 30 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 279 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #