data_4XVR # _model_server_result.job_id uGh1GlDhLxbe2xXIyMlIsg _model_server_result.datetime_utc '2024-10-24 04:28:04' _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 4xvr # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":202}' # _entry.id 4XVR # _exptl.entry_id 4XVR _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 90 _cell.angle_gamma 120 _cell.entry_id 4XVR _cell.length_a 39.234 _cell.length_b 39.234 _cell.length_c 157.204 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4XVR _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 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 _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 OG SER 17 A SER 17 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.857 ? metalc ? metalc2 A OG1 THR 35 A THR 35 1_555 B MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.215 ? metalc ? metalc3 A O ARG 102 A ARG 102 1_555 D CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.558 ? metalc ? metalc4 A OD1 ASP 105 A ASP 105 1_555 D CA CA . A CA 203 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.667 ? metalc ? metalc5 B MG MG . A MG 201 1_555 C O1B GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.07 ? metalc ? metalc6 B MG MG . A MG 201 1_555 C O1G GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.027 ? metalc ? metalc7 B MG MG . A MG 201 1_555 E O HOH . A HOH 309 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.064 ? metalc ? metalc8 B MG MG . A MG 201 1_555 E O HOH . A HOH 328 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.365 ? metalc ? metalc9 D CA CA . A CA 203 1_555 E O HOH . A HOH 316 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.447 ? # _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 4XVR _atom_sites.fract_transf_matrix[1][1] 0.025488 _atom_sites.fract_transf_matrix[1][2] 0.014716 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.029431 _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] 0.006361 _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 1 201 529 MG MG . C 3 GNP A 1 202 528 GNP GNP . D 4 CA A 1 203 530 CA CA . E 5 HOH A 1 301 103 HOH HOH . E 5 HOH A 2 302 149 HOH HOH . E 5 HOH A 3 303 157 HOH HOH . E 5 HOH A 4 304 102 HOH HOH . E 5 HOH A 5 305 132 HOH HOH . E 5 HOH A 6 306 131 HOH HOH . E 5 HOH A 7 307 118 HOH HOH . E 5 HOH A 8 308 110 HOH HOH . E 5 HOH A 9 309 122 HOH HOH . E 5 HOH A 10 310 156 HOH HOH . E 5 HOH A 11 311 112 HOH HOH . E 5 HOH A 12 312 101 HOH HOH . E 5 HOH A 13 313 111 HOH HOH . E 5 HOH A 14 314 120 HOH HOH . E 5 HOH A 15 315 138 HOH HOH . E 5 HOH A 16 316 126 HOH HOH . E 5 HOH A 17 317 136 HOH HOH . E 5 HOH A 18 318 151 HOH HOH . E 5 HOH A 19 319 124 HOH HOH . E 5 HOH A 20 320 113 HOH HOH . E 5 HOH A 21 321 129 HOH HOH . E 5 HOH A 22 322 117 HOH HOH . E 5 HOH A 23 323 154 HOH HOH . E 5 HOH A 24 324 133 HOH HOH . E 5 HOH A 25 325 152 HOH HOH . E 5 HOH A 26 326 104 HOH HOH . E 5 HOH A 27 327 105 HOH HOH . E 5 HOH A 28 328 106 HOH HOH . E 5 HOH A 29 329 107 HOH HOH . E 5 HOH A 30 330 108 HOH HOH . E 5 HOH A 31 331 114 HOH HOH . E 5 HOH A 32 332 123 HOH HOH . E 5 HOH A 33 333 130 HOH HOH . E 5 HOH A 34 334 139 HOH HOH . E 5 HOH A 35 335 140 HOH HOH . E 5 HOH A 36 336 141 HOH HOH . E 5 HOH A 37 337 142 HOH HOH . E 5 HOH A 38 338 145 HOH HOH . E 5 HOH A 39 339 147 HOH HOH . E 5 HOH A 40 340 148 HOH HOH . E 5 HOH A 41 341 150 HOH HOH . E 5 HOH A 42 342 158 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 -5.149 -14.461 -4.659 1 44.16 ? PG GNP 202 A 1 HETATM 2 O O1G GNP . . . C 3 -6.196 -14.609 -5.73 1 37.88 ? O1G GNP 202 A 1 HETATM 3 O O2G GNP . . . C 3 -5.71 -14.358 -3.252 1 43.15 ? O2G GNP 202 A 1 HETATM 4 O O3G GNP . . . C 3 -4.121 -15.581 -4.58 1 41.09 ? O3G GNP 202 A 1 HETATM 5 N N3B GNP . . . C 3 -4.335 -13.132 -4.939 1 41.15 ? N3B GNP 202 A 1 HETATM 6 P PB GNP . . . C 3 -3.71 -12.71 -6.338 1 40.61 ? PB GNP 202 A 1 HETATM 7 O O1B GNP . . . C 3 -4.697 -12.984 -7.403 1 39.28 ? O1B GNP 202 A 1 HETATM 8 O O2B GNP . . . C 3 -2.362 -13.325 -6.448 1 36.78 ? O2B GNP 202 A 1 HETATM 9 O O3A GNP . . . C 3 -3.488 -11.192 -6.259 1 38.99 ? O3A GNP 202 A 1 HETATM 10 P PA GNP . . . C 3 -4.435 -10.085 -6.715 1 43.3 ? PA GNP 202 A 1 HETATM 11 O O1A GNP . . . C 3 -4.509 -10.016 -8.189 1 40.01 ? O1A GNP 202 A 1 HETATM 12 O O2A GNP . . . C 3 -5.74 -10.142 -6 1 40.64 ? O2A GNP 202 A 1 HETATM 13 O O5' GNP . . . C 3 -3.687 -8.772 -6.262 1 40.55 ? O5' GNP 202 A 1 HETATM 14 C C5' GNP . . . C 3 -3.355 -8.566 -4.881 1 40.81 ? C5' GNP 202 A 1 HETATM 15 C C4' GNP . . . C 3 -3.143 -7.08 -4.583 1 39.15 ? C4' GNP 202 A 1 HETATM 16 O O4' GNP . . . C 3 -2.004 -6.585 -5.34 1 41.02 ? O4' GNP 202 A 1 HETATM 17 C C3' GNP . . . C 3 -4.282 -6.134 -4.951 1 44.44 ? C3' GNP 202 A 1 HETATM 18 O O3' GNP . . . C 3 -4.261 -4.97 -4.136 1 39.84 ? O3' GNP 202 A 1 HETATM 19 C C2' GNP . . . C 3 -3.921 -5.738 -6.381 1 46.26 ? C2' GNP 202 A 1 HETATM 20 O O2' GNP . . . C 3 -4.607 -4.571 -6.831 1 46.41 ? O2' GNP 202 A 1 HETATM 21 C C1' GNP . . . C 3 -2.405 -5.556 -6.224 1 42.46 ? C1' GNP 202 A 1 HETATM 22 N N9 GNP . . . C 3 -1.677 -5.697 -7.49 1 44.49 ? N9 GNP 202 A 1 HETATM 23 C C8 GNP . . . C 3 -1.806 -6.732 -8.387 1 39.68 ? C8 GNP 202 A 1 HETATM 24 N N7 GNP . . . C 3 -1.047 -6.604 -9.443 1 42.4 ? N7 GNP 202 A 1 HETATM 25 C C5 GNP . . . C 3 -0.376 -5.402 -9.247 1 40.66 ? C5 GNP 202 A 1 HETATM 26 C C6 GNP . . . C 3 0.579 -4.744 -10.062 1 38.45 ? C6 GNP 202 A 1 HETATM 27 O O6 GNP . . . C 3 1.039 -5.101 -11.16 1 36.93 ? O6 GNP 202 A 1 HETATM 28 N N1 GNP . . . C 3 1.001 -3.545 -9.489 1 39.53 ? N1 GNP 202 A 1 HETATM 29 C C2 GNP . . . C 3 0.567 -3.059 -8.278 1 42.53 ? C2 GNP 202 A 1 HETATM 30 N N2 GNP . . . C 3 1.087 -1.886 -7.868 1 46.01 ? N2 GNP 202 A 1 HETATM 31 N N3 GNP . . . C 3 -0.315 -3.68 -7.51 1 43.4 ? N3 GNP 202 A 1 HETATM 32 C C4 GNP . . . C 3 -0.751 -4.834 -8.049 1 38.83 ? C4 GNP 202 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 295 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #