data_5KHO # _model_server_result.job_id QXDJ4XJ6BUIEnVxL2DBtUA _model_server_result.datetime_utc '2024-11-24 10:52:48' _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 5kho # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"G","auth_seq_id":201}' # _entry.id 5KHO # _exptl.entry_id 5KHO _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 5 _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 90 _cell.angle_beta 90 _cell.angle_gamma 90 _cell.entry_id 5KHO _cell.length_a 101.54 _cell.length_b 154.76 _cell.length_c 38.8 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5KHO _symmetry.cell_setting ? _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 2' # _pdbx_struct_assembly.method_details ? _pdbx_struct_assembly.oligomeric_details tetrameric _pdbx_struct_assembly.oligomeric_count 4 _pdbx_struct_assembly.details author_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D,E,F,G,H,I,J,K,L,M _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 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 5 G N N ? 5 I 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 C OG SER 17 C SER 17 1_555 F MG MG . C MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.496 ? metalc ? metalc2 C OG1 THR 35 C THR 35 1_555 F MG MG . C MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.252 ? metalc ? metalc3 F MG MG . C MG 200 1_555 G O2B GNP . C GNP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.917 ? metalc ? metalc4 F MG MG . C MG 200 1_555 G O2G GNP . C GNP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.847 ? metalc ? metalc5 F MG MG . C MG 200 1_555 L O HOH . C HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.181 ? metalc ? metalc6 F MG MG . C MG 200 1_555 L O HOH . C HOH 303 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc7 D OG SER 17 D SER 17 1_555 H MG MG . D MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.127 ? metalc ? metalc8 D OG1 THR 35 D THR 35 1_555 H MG MG . D MG 200 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.223 ? metalc ? metalc9 H MG MG . D MG 200 1_555 I O1G GNP . D GNP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.075 ? metalc ? metalc10 H MG MG . D MG 200 1_555 I O1B GNP . D GNP 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc11 H MG MG . D MG 200 1_555 M O HOH . D HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.976 ? metalc ? metalc12 H MG MG . D MG 200 1_555 M O HOH . D HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.932 ? # _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 5KHO _atom_sites.fract_transf_matrix[1][1] 0.009848 _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] 0.006462 _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] 0.025773 _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 E 3 GOL A 1 301 1 GOL GOL . F 4 MG C 1 200 200 MG MG . G 5 GNP C 1 201 201 GNP GNP . H 4 MG D 1 200 200 MG MG . I 5 GNP D 1 201 201 GNP GNP . J 6 HOH A 1 401 2 HOH HOH . J 6 HOH A 2 402 11 HOH HOH . K 6 HOH B 1 301 3 HOH HOH . L 6 HOH C 1 301 13 HOH HOH . L 6 HOH C 2 302 4 HOH HOH . L 6 HOH C 3 303 5 HOH HOH . L 6 HOH C 4 304 6 HOH HOH . M 6 HOH D 1 301 8 HOH HOH . M 6 HOH D 2 302 7 HOH HOH . M 6 HOH D 3 303 14 HOH HOH . M 6 HOH D 4 304 9 HOH HOH . M 6 HOH D 5 305 1 HOH HOH . M 6 HOH D 6 306 10 HOH HOH . M 6 HOH D 7 307 12 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 . . . G 5 -46.254 28.486 -26.063 1 81.42 ? PG GNP 201 C 1 HETATM 2 O O1G GNP . . . G 5 -45.609 29.56 -27.076 1 91.39 ? O1G GNP 201 C 1 HETATM 3 O O2G GNP . . . G 5 -45.286 28.284 -24.807 1 78.36 ? O2G GNP 201 C 1 HETATM 4 O O3G GNP . . . G 5 -46.433 27.175 -26.722 1 78.29 ? O3G GNP 201 C 1 HETATM 5 N N3B GNP . . . G 5 -47.765 29.137 -25.498 1 77.39 ? N3B GNP 201 C 1 HETATM 6 P PB GNP . . . G 5 -48.824 28.104 -24.596 1 71.21 ? PB GNP 201 C 1 HETATM 7 O O1B GNP . . . G 5 -49.372 27.076 -25.505 1 77.74 ? O1B GNP 201 C 1 HETATM 8 O O2B GNP . . . G 5 -48.002 27.386 -23.435 1 78.22 ? O2B GNP 201 C 1 HETATM 9 O O3A GNP . . . G 5 -50.007 28.974 -23.962 1 72.77 ? O3A GNP 201 C 1 HETATM 10 P PA GNP . . . G 5 -49.869 29.677 -22.523 1 71.42 ? PA GNP 201 C 1 HETATM 11 O O1A GNP . . . G 5 -48.574 30.426 -22.449 1 75.08 ? O1A GNP 201 C 1 HETATM 12 O O2A GNP . . . G 5 -50.205 28.668 -21.453 1 78.48 ? O2A GNP 201 C 1 HETATM 13 O O5' GNP . . . G 5 -51.065 30.745 -22.582 1 74.73 ? O5' GNP 201 C 1 HETATM 14 C C5' GNP . . . G 5 -51.091 31.854 -23.495 1 69.89 ? C5' GNP 201 C 1 HETATM 15 C C4' GNP . . . G 5 -52.103 32.896 -23.016 1 68.2 ? C4' GNP 201 C 1 HETATM 16 O O4' GNP . . . G 5 -53.394 32.296 -23.003 1 71.69 ? O4' GNP 201 C 1 HETATM 17 C C3' GNP . . . G 5 -51.863 33.363 -21.583 1 70.3 ? C3' GNP 201 C 1 HETATM 18 O O3' GNP . . . G 5 -52.229 34.731 -21.45 1 74.22 ? O3' GNP 201 C 1 HETATM 19 C C2' GNP . . . G 5 -52.806 32.531 -20.749 1 69.98 ? C2' GNP 201 C 1 HETATM 20 O O2' GNP . . . G 5 -53.143 33.18 -19.534 1 73.06 ? O2' GNP 201 C 1 HETATM 21 C C1' GNP . . . G 5 -53.978 32.388 -21.697 1 73.82 ? C1' GNP 201 C 1 HETATM 22 N N9 GNP . . . G 5 -54.792 31.188 -21.411 1 79.99 ? N9 GNP 201 C 1 HETATM 23 C C8 GNP . . . G 5 -54.391 29.897 -21.426 1 78.44 ? C8 GNP 201 C 1 HETATM 24 N N7 GNP . . . G 5 -55.424 29.069 -21.126 1 78.93 ? N7 GNP 201 C 1 HETATM 25 C C5 GNP . . . G 5 -56.508 29.839 -20.913 1 79.56 ? C5 GNP 201 C 1 HETATM 26 C C6 GNP . . . G 5 -57.934 29.622 -20.562 1 81.23 ? C6 GNP 201 C 1 HETATM 27 O O6 GNP . . . G 5 -58.386 28.473 -20.377 1 83.37 ? O6 GNP 201 C 1 HETATM 28 N N1 GNP . . . G 5 -58.723 30.704 -20.453 1 83.94 ? N1 GNP 201 C 1 HETATM 29 C C2 GNP . . . G 5 -58.277 31.966 -20.651 1 81.04 ? C2 GNP 201 C 1 HETATM 30 N N2 GNP . . . G 5 -59.138 32.996 -20.513 1 78.65 ? N2 GNP 201 C 1 HETATM 31 N N3 GNP . . . G 5 -56.988 32.24 -20.978 1 79.63 ? N3 GNP 201 C 1 HETATM 32 C C4 GNP . . . G 5 -56.084 31.237 -21.114 1 80.09 ? C4 GNP 201 C 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 18 _model_server_stats.create_model_time_ms 5 _model_server_stats.query_time_ms 232 _model_server_stats.encode_time_ms 1 _model_server_stats.element_count 32 #