data_3PIT # _model_server_result.job_id MjNamIn6MA3or_w-AYjEhw _model_server_result.datetime_utc '2024-11-18 02:21:36' _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 3pit # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":179}' # _entry.id 3PIT # _exptl.entry_id 3PIT _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 522.196 _entity.id 2 _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 90 _cell.entry_id 3PIT _cell.length_a 47.111 _cell.length_b 89.646 _cell.length_c 41.273 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3PIT _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 monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details software_defined_assembly _pdbx_struct_assembly.id 1 # _pdbx_struct_assembly_gen.asym_id_list A,B,C,D _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 2 _struct_asym.id B _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 32 A SER 27 1_555 C MG MG . A MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.051 ? metalc ? metalc2 A OG1 THR 50 A THR 45 1_555 C MG MG . A MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.088 ? metalc ? metalc3 B O2G GNP . A GNP 179 1_555 C MG MG . A MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? metalc ? metalc4 B O2B GNP . A GNP 179 1_555 C MG MG . A MG 180 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.058 ? metalc ? metalc5 C MG MG . A MG 180 1_555 D O HOH . A HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.155 ? metalc ? metalc6 C MG MG . A MG 180 1_555 D O HOH . A HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.056 ? # _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 116 n n PG O2G GNP sing 117 n n PG O3G GNP sing 118 n n PG N3B GNP sing 119 n n O2G HOG2 GNP sing 120 n n O3G HOG3 GNP sing 121 n n N3B PB GNP sing 122 n n N3B HNB3 GNP sing 123 n n PB O1B GNP doub 124 n n PB O2B GNP sing 125 n n PB O3A GNP sing 126 n n O2B HOB2 GNP sing 127 n n O3A PA GNP sing 128 n n PA O1A GNP doub 129 n n PA O2A GNP sing 130 n n PA O5' GNP sing 131 n n O2A HOA2 GNP sing 132 n n O5' C5' GNP sing 133 n n C5' C4' GNP sing 134 n n C5' "H5'2" GNP sing 135 n n C5' "H5'1" GNP sing 136 n n C4' O4' GNP sing 137 n n C4' C3' GNP sing 138 n n C4' H4' GNP sing 139 n n O4' C1' GNP sing 140 n n C3' O3' GNP sing 141 n n C3' C2' GNP sing 142 n n C3' H3' GNP sing 143 n n O3' HO3' GNP sing 144 n n C2' O2' GNP sing 145 n n C2' C1' GNP sing 146 n n C2' H2' GNP sing 147 n n O2' HO2' GNP sing 148 n n C1' N9 GNP sing 149 n n C1' H1' GNP sing 150 n n N9 C8 GNP sing 151 n y N9 C4 GNP sing 152 n y C8 N7 GNP doub 153 n y C8 H8 GNP sing 154 n n N7 C5 GNP sing 155 n y C5 C6 GNP sing 156 n y C5 C4 GNP doub 157 n y C6 O6 GNP doub 158 n n C6 N1 GNP sing 159 n y N1 C2 GNP sing 160 n y N1 HN1 GNP sing 161 n n C2 N2 GNP sing 162 n n C2 N3 GNP doub 163 n y N2 HN21 GNP sing 164 n n N2 HN22 GNP sing 165 n n N3 C4 GNP sing 166 n y # _atom_sites.entry_id 3PIT _atom_sites.fract_transf_matrix[1][1] 0.021226 _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] 0.011155 _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] 0.024229 _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 GNP A 1 179 179 GNP GNP . C 3 MG A 1 180 180 MG MG . D 4 HOH A 1 1001 1001 HOH HOH . D 4 HOH A 2 1002 1002 HOH HOH . D 4 HOH A 3 1003 1003 HOH HOH . D 4 HOH A 4 1004 1004 HOH HOH . D 4 HOH A 5 1005 1005 HOH HOH . D 4 HOH A 6 1006 1006 HOH HOH . D 4 HOH A 7 1007 1007 HOH HOH . D 4 HOH A 8 1008 1008 HOH HOH . D 4 HOH A 9 1009 1009 HOH HOH . D 4 HOH A 10 1010 1010 HOH HOH . D 4 HOH A 11 1011 1011 HOH HOH . D 4 HOH A 12 1012 1012 HOH HOH . D 4 HOH A 13 1013 1013 HOH HOH . D 4 HOH A 14 1014 1014 HOH HOH . D 4 HOH A 15 1015 1015 HOH HOH . D 4 HOH A 16 1016 1016 HOH HOH . D 4 HOH A 17 1017 1017 HOH HOH . D 4 HOH A 18 1018 1018 HOH HOH . D 4 HOH A 19 1019 1019 HOH HOH . D 4 HOH A 20 1020 1020 HOH HOH . D 4 HOH A 21 1021 1021 HOH HOH . D 4 HOH A 22 1022 1022 HOH HOH . D 4 HOH A 23 1023 1023 HOH HOH . D 4 HOH A 24 1024 1024 HOH HOH . D 4 HOH A 25 1025 1025 HOH HOH . D 4 HOH A 26 1026 1026 HOH HOH . D 4 HOH A 27 1027 1027 HOH HOH . D 4 HOH A 28 1028 1028 HOH HOH . D 4 HOH A 29 1029 1029 HOH HOH . D 4 HOH A 30 1030 1030 HOH HOH . D 4 HOH A 31 1031 1031 HOH HOH . D 4 HOH A 32 1032 1032 HOH HOH . D 4 HOH A 33 1033 1033 HOH HOH . D 4 HOH A 34 1034 1034 HOH HOH . D 4 HOH A 35 1035 1035 HOH HOH . D 4 HOH A 36 1036 1036 HOH HOH . D 4 HOH A 37 1037 1037 HOH HOH . D 4 HOH A 38 1038 1038 HOH HOH . D 4 HOH A 39 1039 1039 HOH HOH . D 4 HOH A 40 1040 1040 HOH HOH . D 4 HOH A 41 1041 1041 HOH HOH . D 4 HOH A 42 1042 1042 HOH HOH . D 4 HOH A 43 1043 1043 HOH HOH . D 4 HOH A 44 1044 1044 HOH HOH . D 4 HOH A 45 1045 1045 HOH HOH . D 4 HOH A 46 1046 1046 HOH HOH . D 4 HOH A 47 1047 1047 HOH HOH . D 4 HOH A 48 1048 1048 HOH HOH . D 4 HOH A 49 1049 1049 HOH HOH . D 4 HOH A 50 1050 1050 HOH HOH . D 4 HOH A 51 1051 1051 HOH HOH . D 4 HOH A 52 1052 1052 HOH HOH . D 4 HOH A 53 1053 1053 HOH HOH . D 4 HOH A 54 1054 1054 HOH HOH . D 4 HOH A 55 1055 1055 HOH HOH . D 4 HOH A 56 1056 1056 HOH HOH . D 4 HOH A 57 1057 1057 HOH HOH . D 4 HOH A 58 1058 1058 HOH HOH . D 4 HOH A 59 1059 1059 HOH HOH . D 4 HOH A 60 1060 1060 HOH HOH . D 4 HOH A 61 1061 1061 HOH HOH . D 4 HOH A 62 1062 1062 HOH HOH . D 4 HOH A 63 1063 1063 HOH HOH . D 4 HOH A 64 1064 1064 HOH HOH . D 4 HOH A 65 1065 1065 HOH HOH . D 4 HOH A 66 1066 1066 HOH HOH . D 4 HOH A 67 1067 1067 HOH HOH . D 4 HOH A 68 1068 1068 HOH HOH . D 4 HOH A 69 1069 1069 HOH HOH . D 4 HOH A 70 1070 1070 HOH HOH . D 4 HOH A 71 1071 1071 HOH HOH . D 4 HOH A 72 1072 1072 HOH HOH . D 4 HOH A 73 1073 1073 HOH HOH . D 4 HOH A 74 1074 1074 HOH HOH . D 4 HOH A 75 1075 1075 HOH HOH . D 4 HOH A 76 1076 1076 HOH HOH . D 4 HOH A 77 1077 1077 HOH HOH . D 4 HOH A 78 1078 1078 HOH HOH . D 4 HOH A 79 1079 1079 HOH HOH . D 4 HOH A 80 1080 1080 HOH HOH . D 4 HOH A 81 1081 1081 HOH HOH . D 4 HOH A 82 1082 1082 HOH HOH . D 4 HOH A 83 1083 1083 HOH HOH . D 4 HOH A 84 1084 1084 HOH HOH . D 4 HOH A 85 1085 1085 HOH HOH . D 4 HOH A 86 1086 1086 HOH HOH . D 4 HOH A 87 1087 1087 HOH HOH . D 4 HOH A 88 1088 1088 HOH HOH . D 4 HOH A 89 1089 1089 HOH HOH . D 4 HOH A 90 1090 1090 HOH HOH . D 4 HOH A 91 1091 1091 HOH HOH . D 4 HOH A 92 1092 1092 HOH HOH . D 4 HOH A 93 1093 1093 HOH HOH . D 4 HOH A 94 1094 1094 HOH HOH . D 4 HOH A 95 1095 1095 HOH HOH . D 4 HOH A 96 1096 1096 HOH HOH . D 4 HOH A 97 1097 1097 HOH HOH . D 4 HOH A 98 1098 1098 HOH HOH . D 4 HOH A 99 1099 1099 HOH HOH . D 4 HOH A 100 1100 1100 HOH HOH . D 4 HOH A 101 1101 1101 HOH HOH . D 4 HOH A 102 1102 1102 HOH HOH . D 4 HOH A 103 1103 1103 HOH HOH . D 4 HOH A 104 1104 1104 HOH HOH . D 4 HOH A 105 1105 1105 HOH HOH . D 4 HOH A 106 1106 1106 HOH HOH . D 4 HOH A 107 1107 1107 HOH HOH . D 4 HOH A 108 1108 1108 HOH HOH . D 4 HOH A 109 1109 1109 HOH HOH . D 4 HOH A 110 1110 1110 HOH HOH . D 4 HOH A 111 1111 1111 HOH HOH . D 4 HOH A 112 1112 1112 HOH HOH . D 4 HOH A 113 1113 1113 HOH HOH . D 4 HOH A 114 1114 1114 HOH HOH . D 4 HOH A 115 1115 1115 HOH HOH . D 4 HOH A 116 1116 1116 HOH HOH . D 4 HOH A 117 1117 1117 HOH HOH . D 4 HOH A 118 1118 1118 HOH HOH . D 4 HOH A 119 1119 1119 HOH HOH . D 4 HOH A 120 1120 1120 HOH HOH . D 4 HOH A 121 1121 1121 HOH HOH . D 4 HOH A 122 1122 1122 HOH HOH . D 4 HOH A 123 1123 1123 HOH HOH . D 4 HOH A 124 1124 1124 HOH HOH . D 4 HOH A 125 1125 1125 HOH HOH . D 4 HOH A 126 1126 1126 HOH HOH . D 4 HOH A 127 1127 1127 HOH HOH . D 4 HOH A 128 1128 1128 HOH HOH . D 4 HOH A 129 1129 1129 HOH HOH . D 4 HOH A 130 1130 1130 HOH HOH . D 4 HOH A 131 1131 1131 HOH HOH . D 4 HOH A 132 1132 1132 HOH HOH . D 4 HOH A 133 1133 1133 HOH HOH . D 4 HOH A 134 1134 1134 HOH HOH . D 4 HOH A 135 1135 1135 HOH HOH . D 4 HOH A 136 1136 1136 HOH HOH . D 4 HOH A 137 1137 1137 HOH HOH . D 4 HOH A 138 1138 1138 HOH HOH . D 4 HOH A 139 1139 1139 HOH HOH . D 4 HOH A 140 1140 1140 HOH HOH . D 4 HOH A 141 1141 1141 HOH HOH . D 4 HOH A 142 1142 1142 HOH HOH . D 4 HOH A 143 1143 1143 HOH HOH . D 4 HOH A 144 1144 1144 HOH HOH . D 4 HOH A 145 1145 1145 HOH HOH . D 4 HOH A 146 1146 1146 HOH HOH . D 4 HOH A 147 1147 1147 HOH HOH . D 4 HOH A 148 1148 1148 HOH HOH . D 4 HOH A 149 1149 1149 HOH HOH . D 4 HOH A 150 1150 1150 HOH HOH . D 4 HOH A 151 1151 1151 HOH HOH . D 4 HOH A 152 1152 1152 HOH HOH . D 4 HOH A 153 1153 1153 HOH HOH . D 4 HOH A 154 1154 1154 HOH HOH . D 4 HOH A 155 1155 1155 HOH HOH . D 4 HOH A 156 1156 1156 HOH HOH . D 4 HOH A 157 1157 1157 HOH HOH . D 4 HOH A 158 1158 1158 HOH HOH . D 4 HOH A 159 1159 1159 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 . . . B 2 -5.541 -1.392 5.896 1 6.19 ? PG GNP 179 A 1 HETATM 2 O O1G GNP . . . B 2 -6.335 -0.469 6.842 1 7.53 ? O1G GNP 179 A 1 HETATM 3 O O2G GNP . . . B 2 -4.526 -0.581 5.154 1 6.81 ? O2G GNP 179 A 1 HETATM 4 O O3G GNP . . . B 2 -6.521 -2.164 5.095 1 6.32 ? O3G GNP 179 A 1 HETATM 5 N N3B GNP . . . B 2 -4.744 -2.445 6.862 1 5.68 ? N3B GNP 179 A 1 HETATM 6 P PB GNP . . . B 2 -3.638 -3.55 6.371 1 5.9 ? PB GNP 179 A 1 HETATM 7 O O1B GNP . . . B 2 -4.314 -4.697 5.686 1 5.92 ? O1B GNP 179 A 1 HETATM 8 O O2B GNP . . . B 2 -2.567 -2.837 5.61 1 5.31 ? O2B GNP 179 A 1 HETATM 9 O O3A GNP . . . B 2 -2.967 -4.119 7.672 1 6.5 ? O3A GNP 179 A 1 HETATM 10 P PA GNP . . . B 2 -1.723 -3.605 8.473 1 6.45 ? PA GNP 179 A 1 HETATM 11 O O1A GNP . . . B 2 -1.953 -2.162 8.774 1 8.36 ? O1A GNP 179 A 1 HETATM 12 O O2A GNP . . . B 2 -0.544 -3.971 7.72 1 8.2 ? O2A GNP 179 A 1 HETATM 13 O O5' GNP . . . B 2 -1.751 -4.48 9.777 1 6.94 ? O5' GNP 179 A 1 HETATM 14 C C5' GNP . . . B 2 -2.824 -4.36 10.71 1 7.63 ? C5' GNP 179 A 1 HETATM 15 C C4' GNP . . . B 2 -2.308 -4.735 12.085 1 7.32 ? C4' GNP 179 A 1 HETATM 16 O O4' GNP . . . B 2 -1.967 -6.151 12.034 1 7.29 ? O4' GNP 179 A 1 HETATM 17 C C3' GNP . . . B 2 -1.052 -3.994 12.549 1 7.75 ? C3' GNP 179 A 1 HETATM 18 O O3' GNP . . . B 2 -1.153 -3.812 13.967 1 9.87 ? O3' GNP 179 A 1 HETATM 19 C C2' GNP . . . B 2 0.08 -4.952 12.146 1 6.93 ? C2' GNP 179 A 1 HETATM 20 O O2' GNP . . . B 2 1.222 -4.89 12.983 1 7.79 ? O2' GNP 179 A 1 HETATM 21 C C1' GNP . . . B 2 -0.607 -6.294 12.379 1 8.14 ? C1' GNP 179 A 1 HETATM 22 N N9 GNP . . . B 2 -0.079 -7.382 11.555 1 8.06 ? N9 GNP 179 A 1 HETATM 23 C C8 GNP . . . B 2 0.026 -7.412 10.177 1 7.21 ? C8 GNP 179 A 1 HETATM 24 N N7 GNP . . . B 2 0.53 -8.543 9.732 1 6.88 ? N7 GNP 179 A 1 HETATM 25 C C5 GNP . . . B 2 0.768 -9.283 10.879 1 7.06 ? C5 GNP 179 A 1 HETATM 26 C C6 GNP . . . B 2 1.284 -10.596 11.013 1 7.07 ? C6 GNP 179 A 1 HETATM 27 O O6 GNP . . . B 2 1.666 -11.354 10.111 1 7.2 ? O6 GNP 179 A 1 HETATM 28 N N1 GNP . . . B 2 1.379 -10.977 12.342 1 6.26 ? N1 GNP 179 A 1 HETATM 29 C C2 GNP . . . B 2 0.978 -10.226 13.433 1 6.8 ? C2 GNP 179 A 1 HETATM 30 N N2 GNP . . . B 2 1.129 -10.762 14.657 1 10.07 ? N2 GNP 179 A 1 HETATM 31 N N3 GNP . . . B 2 0.476 -8.999 13.316 1 7.42 ? N3 GNP 179 A 1 HETATM 32 C C4 GNP . . . B 2 0.399 -8.605 12.015 1 7.9 ? C4 GNP 179 A 1 # _model_server_stats.io_time_ms 50 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 18 _model_server_stats.query_time_ms 335 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #