data_5LPN # _model_server_result.job_id -MgV1LAS1pnoZLFRFZbBiA _model_server_result.datetime_utc '2024-11-22 00:00:01' _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 5lpn # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"E","auth_seq_id":202}' # _entry.id 5LPN # _exptl.entry_id 5LPN _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 4 _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 5LPN _cell.length_a 58.39 _cell.length_b 59 _cell.length_c 198.18 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 5LPN _symmetry.cell_setting ? _symmetry.Int_Tables_number 19 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 21 21 21' # _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 _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 ? 4 E N N ? 4 G 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 OG1 THR 25 A THR 23 1_555 D MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.937 ? metalc ? metalc2 A OG1 THR 43 A THR 41 1_555 D MG MG . A MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.987 ? metalc ? metalc3 D MG MG . A MG 201 1_555 E O3G GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.929 ? metalc ? metalc4 D MG MG . A MG 201 1_555 E O2B GNP . A GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.379 ? metalc ? metalc5 D MG MG . A MG 201 1_555 H O HOH . A HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.118 ? metalc ? metalc6 D MG MG . A MG 201 1_555 H O HOH . A HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.944 ? metalc ? metalc7 C OG1 THR 25 C THR 23 1_555 F MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.983 ? metalc ? metalc8 C OG1 THR 43 C THR 41 1_555 F MG MG . C MG 201 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.004 ? metalc ? metalc9 F MG MG . C MG 201 1_555 G O2G GNP . C GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.916 ? metalc ? metalc10 F MG MG . C MG 201 1_555 G O1B GNP . C GNP 202 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? metalc ? metalc11 F MG MG . C MG 201 1_555 I O HOH . C HOH 301 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.385 ? metalc ? metalc12 F MG MG . C MG 201 1_555 I O HOH . C HOH 302 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? # _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 5LPN _atom_sites.fract_transf_matrix[1][1] 0.017126 _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] 0.016949 _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] 0.005046 _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 MG A 1 201 400 MG MG . E 4 GNP A 1 202 500 GNP GNP . F 3 MG C 1 201 400 MG MG . G 4 GNP C 1 202 500 GNP GNP . H 5 HOH A 1 301 1 HOH HOH . H 5 HOH A 2 302 2 HOH HOH . I 5 HOH C 1 301 4 HOH HOH . I 5 HOH C 2 302 3 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 . . . E 4 -10.959 59.34 192.163 1 59.34 ? PG GNP 202 A 1 HETATM 2 O O1G GNP . . . E 4 -12.216 59.15 191.346 1 53.78 ? O1G GNP 202 A 1 HETATM 3 O O2G GNP . . . E 4 -10.571 60.775 192.432 1 53.67 ? O2G GNP 202 A 1 HETATM 4 O O3G GNP . . . E 4 -10.972 58.674 193.514 1 64.39 ? O3G GNP 202 A 1 HETATM 5 N N3B GNP . . . E 4 -9.8 58.634 191.343 1 63.94 ? N3B GNP 202 A 1 HETATM 6 P PB GNP . . . E 4 -8.269 58.702 191.754 1 57.5 ? PB GNP 202 A 1 HETATM 7 O O1B GNP . . . E 4 -7.692 60.003 191.346 1 51.74 ? O1B GNP 202 A 1 HETATM 8 O O2B GNP . . . E 4 -8.151 58.35 193.188 1 54.16 ? O2B GNP 202 A 1 HETATM 9 O O3A GNP . . . E 4 -7.569 57.619 190.927 1 69.12 ? O3A GNP 202 A 1 HETATM 10 P PA GNP . . . E 4 -7.467 56.18 191.422 1 66.73 ? PA GNP 202 A 1 HETATM 11 O O1A GNP . . . E 4 -8.735 55.774 192.071 1 82.81 ? O1A GNP 202 A 1 HETATM 12 O O2A GNP . . . E 4 -6.229 56.078 192.227 1 62.75 ? O2A GNP 202 A 1 HETATM 13 O O5' GNP . . . E 4 -7.274 55.183 190.215 1 59.07 ? O5' GNP 202 A 1 HETATM 14 C C5' GNP . . . E 4 -6.794 55.585 188.939 1 80.72 ? C5' GNP 202 A 1 HETATM 15 C C4' GNP . . . E 4 -6.798 54.367 188.029 1 74.21 ? C4' GNP 202 A 1 HETATM 16 O O4' GNP . . . E 4 -5.58 54.304 187.243 1 69.39 ? O4' GNP 202 A 1 HETATM 17 C C3' GNP . . . E 4 -6.88 53.05 188.788 1 76.63 ? C3' GNP 202 A 1 HETATM 18 O O3' GNP . . . E 4 -7.704 52.134 188.083 1 87.77 ? O3' GNP 202 A 1 HETATM 19 C C2' GNP . . . E 4 -5.433 52.568 188.864 1 88.46 ? C2' GNP 202 A 1 HETATM 20 O O2' GNP . . . E 4 -5.344 51.16 188.761 1 107.85 ? O2' GNP 202 A 1 HETATM 21 C C1' GNP . . . E 4 -4.748 53.24 187.674 1 77.44 ? C1' GNP 202 A 1 HETATM 22 N N9 GNP . . . E 4 -3.443 53.799 188.026 1 80.22 ? N9 GNP 202 A 1 HETATM 23 C C8 GNP . . . E 4 -3.18 54.576 189.131 1 80.19 ? C8 GNP 202 A 1 HETATM 24 N N7 GNP . . . E 4 -1.936 54.954 189.224 1 78.66 ? N7 GNP 202 A 1 HETATM 25 C C5 GNP . . . E 4 -1.326 54.394 188.106 1 73.45 ? C5 GNP 202 A 1 HETATM 26 C C6 GNP . . . E 4 0.024 54.464 187.681 1 76.6 ? C6 GNP 202 A 1 HETATM 27 O O6 GNP . . . E 4 0.976 55.054 188.212 1 87.13 ? O6 GNP 202 A 1 HETATM 28 N N1 GNP . . . E 4 0.229 53.764 186.497 1 87.32 ? N1 GNP 202 A 1 HETATM 29 C C2 GNP . . . E 4 -0.743 53.076 185.814 1 84.56 ? C2 GNP 202 A 1 HETATM 30 N N2 GNP . . . E 4 -0.335 52.463 184.692 1 80.83 ? N2 GNP 202 A 1 HETATM 31 N N3 GNP . . . E 4 -2.013 52.999 186.202 1 81.12 ? N3 GNP 202 A 1 HETATM 32 C C4 GNP . . . E 4 -2.237 53.679 187.356 1 76.44 ? C4 GNP 202 A 1 # _model_server_stats.io_time_ms 18 _model_server_stats.parse_time_ms 19 _model_server_stats.create_model_time_ms 28 _model_server_stats.query_time_ms 344 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 32 #