data_3KKM # _model_server_result.job_id w0OBo30GtWMqsk1Mcggm5A _model_server_result.datetime_utc '2024-10-12 12:22:47' _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 3kkm # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":167}' # _entry.id 3KKM # _exptl.entry_id 3KKM _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 120 _cell.entry_id 3KKM _cell.length_a 92.855 _cell.length_b 92.855 _cell.length_c 117.478 _cell.Z_PDB 18 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3KKM _symmetry.cell_setting ? _symmetry.Int_Tables_number 155 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'H 3 2' # _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,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 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 23 A SER 17 1_555 C MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.105 ? metalc ? metalc2 B O2G GNP . A GNP 167 1_555 C MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.011 ? metalc ? metalc3 B O2B GNP . A GNP 167 1_555 C MG MG . A MG 168 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.146 ? metalc ? metalc4 C MG MG . A MG 168 1_555 F O HOH . A HOH 1001 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.022 ? metalc ? metalc5 C MG MG . A MG 168 1_555 F O HOH . A HOH 1002 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.272 ? metalc ? metalc6 C MG MG . A MG 168 1_555 F O HOH . A HOH 1003 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.159 ? # _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 3KKM _atom_sites.fract_transf_matrix[1][1] 0.010769 _atom_sites.fract_transf_matrix[1][2] 0.006218 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.012436 _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] 0.008512 _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 1 167 167 GNP GNP . C 3 MG A 1 168 168 MG MG . D 4 SO4 A 1 169 169 SO4 SO4 . E 4 SO4 A 1 170 170 SO4 SO4 . F 5 HOH A 1 1001 3001 HOH HOH . F 5 HOH A 2 1002 3002 HOH HOH . F 5 HOH A 3 1003 3003 HOH HOH . F 5 HOH A 4 1004 3004 HOH HOH . F 5 HOH A 5 1005 3005 HOH HOH . F 5 HOH A 6 1006 3006 HOH HOH . F 5 HOH A 7 1007 3007 HOH HOH . F 5 HOH A 8 1008 3008 HOH HOH . F 5 HOH A 9 1009 3009 HOH HOH . F 5 HOH A 10 1010 3010 HOH HOH . F 5 HOH A 11 1011 3011 HOH HOH . F 5 HOH A 12 1012 3012 HOH HOH . F 5 HOH A 13 1013 3013 HOH HOH . F 5 HOH A 14 1014 3014 HOH HOH . F 5 HOH A 15 1015 3015 HOH HOH . F 5 HOH A 16 1016 3016 HOH HOH . F 5 HOH A 17 1017 3017 HOH HOH . F 5 HOH A 18 1018 3018 HOH HOH . F 5 HOH A 19 1019 3019 HOH HOH . F 5 HOH A 20 1020 3020 HOH HOH . F 5 HOH A 21 1021 3021 HOH HOH . F 5 HOH A 22 1022 3022 HOH HOH . F 5 HOH A 23 1023 3023 HOH HOH . F 5 HOH A 24 1024 3024 HOH HOH . F 5 HOH A 25 1025 3025 HOH HOH . F 5 HOH A 26 1026 3026 HOH HOH . F 5 HOH A 27 1027 3027 HOH HOH . F 5 HOH A 28 1028 3028 HOH HOH . F 5 HOH A 29 1029 3029 HOH HOH . F 5 HOH A 30 1030 3030 HOH HOH . F 5 HOH A 31 1031 3031 HOH HOH . F 5 HOH A 32 1032 3032 HOH HOH . F 5 HOH A 33 1033 3033 HOH HOH . F 5 HOH A 34 1034 3034 HOH HOH . F 5 HOH A 35 1035 3035 HOH HOH . F 5 HOH A 36 1036 3036 HOH HOH . F 5 HOH A 37 1037 3037 HOH HOH . F 5 HOH A 38 1038 3038 HOH HOH . F 5 HOH A 39 1039 3039 HOH HOH . F 5 HOH A 40 1040 3040 HOH HOH . F 5 HOH A 41 1041 3041 HOH HOH . F 5 HOH A 42 1042 3042 HOH HOH . F 5 HOH A 43 1043 3043 HOH HOH . F 5 HOH A 44 1044 3044 HOH HOH . F 5 HOH A 45 1045 3045 HOH HOH . F 5 HOH A 46 1046 3046 HOH HOH . F 5 HOH A 47 1047 3047 HOH HOH . F 5 HOH A 48 1048 3048 HOH HOH . F 5 HOH A 49 1049 3049 HOH HOH . F 5 HOH A 50 1050 3050 HOH HOH . F 5 HOH A 51 1051 3051 HOH HOH . F 5 HOH A 52 1052 3052 HOH HOH . F 5 HOH A 53 1053 3053 HOH HOH . F 5 HOH A 54 1054 3054 HOH HOH . F 5 HOH A 55 1055 3055 HOH HOH . F 5 HOH A 56 1056 3056 HOH HOH . F 5 HOH A 57 1057 3057 HOH HOH . F 5 HOH A 58 1058 3058 HOH HOH . F 5 HOH A 59 1059 3059 HOH HOH . F 5 HOH A 60 1060 3060 HOH HOH . F 5 HOH A 61 1061 3061 HOH HOH . F 5 HOH A 62 1062 3062 HOH HOH . F 5 HOH A 63 1063 3063 HOH HOH . F 5 HOH A 64 1064 3064 HOH HOH . F 5 HOH A 65 1065 3065 HOH HOH . F 5 HOH A 66 1066 3066 HOH HOH . F 5 HOH A 67 1067 3067 HOH HOH . F 5 HOH A 68 1068 3068 HOH HOH . F 5 HOH A 69 1069 3069 HOH HOH . F 5 HOH A 70 1070 3070 HOH HOH . F 5 HOH A 71 1071 3071 HOH HOH . F 5 HOH A 72 1072 3072 HOH HOH . F 5 HOH A 73 1073 3073 HOH HOH . F 5 HOH A 74 1074 3074 HOH HOH . F 5 HOH A 75 1075 3075 HOH HOH . F 5 HOH A 76 1076 3076 HOH HOH . F 5 HOH A 77 1077 3077 HOH HOH . F 5 HOH A 78 1078 3078 HOH HOH . F 5 HOH A 79 1079 3079 HOH HOH . F 5 HOH A 80 1080 3080 HOH HOH . F 5 HOH A 81 1081 3081 HOH HOH . F 5 HOH A 82 1082 3082 HOH HOH . F 5 HOH A 83 1083 3083 HOH HOH . F 5 HOH A 84 1084 3084 HOH HOH . F 5 HOH A 85 1085 3085 HOH HOH . F 5 HOH A 86 1086 3086 HOH HOH . F 5 HOH A 87 1087 3087 HOH HOH . F 5 HOH A 88 1088 3088 HOH HOH . F 5 HOH A 89 1089 3089 HOH HOH . F 5 HOH A 90 1090 3090 HOH HOH . F 5 HOH A 91 1091 3091 HOH HOH . F 5 HOH A 92 1092 3092 HOH HOH . F 5 HOH A 93 1093 3093 HOH HOH . F 5 HOH A 94 1094 3094 HOH HOH . F 5 HOH A 95 1095 3095 HOH HOH . F 5 HOH A 96 1096 3096 HOH HOH . F 5 HOH A 97 1097 3097 HOH HOH . F 5 HOH A 98 1098 3098 HOH HOH . F 5 HOH A 99 1099 3099 HOH HOH . F 5 HOH A 100 1100 3100 HOH HOH . F 5 HOH A 101 1101 3101 HOH HOH . F 5 HOH A 102 1102 3102 HOH HOH . F 5 HOH A 103 1103 3103 HOH HOH . F 5 HOH A 104 1104 3104 HOH HOH . F 5 HOH A 105 1105 3105 HOH HOH . F 5 HOH A 106 1106 3106 HOH HOH . F 5 HOH A 107 1107 3107 HOH HOH . F 5 HOH A 108 1108 3108 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 -6.43 -13.77 -17.935 1 18.62 ? PG GNP 167 A 1 HETATM 2 O O1G GNP . . . B 2 -6.584 -12.601 -16.964 1 20.57 ? O1G GNP 167 A 1 HETATM 3 O O2G GNP . . . B 2 -6.865 -15.08 -17.358 1 17.11 ? O2G GNP 167 A 1 HETATM 4 O O3G GNP . . . B 2 -5.01 -13.793 -18.365 1 17.98 ? O3G GNP 167 A 1 HETATM 5 N N3B GNP . . . B 2 -7.374 -13.414 -19.197 1 14.8 ? N3B GNP 167 A 1 HETATM 6 P PB GNP . . . B 2 -7.65 -14.347 -20.501 1 14.4 ? PB GNP 167 A 1 HETATM 7 O O1B GNP . . . B 2 -6.525 -14.297 -21.495 1 14.01 ? O1B GNP 167 A 1 HETATM 8 O O2B GNP . . . B 2 -7.985 -15.732 -20.095 1 11.95 ? O2B GNP 167 A 1 HETATM 9 O O3A GNP . . . B 2 -8.871 -13.762 -21.218 1 12.75 ? O3A GNP 167 A 1 HETATM 10 P PA GNP . . . B 2 -10.395 -14.15 -21.149 1 15.44 ? PA GNP 167 A 1 HETATM 11 O O1A GNP . . . B 2 -10.84 -13.944 -19.737 1 18.23 ? O1A GNP 167 A 1 HETATM 12 O O2A GNP . . . B 2 -10.642 -15.459 -21.765 1 12.72 ? O2A GNP 167 A 1 HETATM 13 O O5' GNP . . . B 2 -11.159 -13.082 -21.995 1 15.7 ? O5' GNP 167 A 1 HETATM 14 C C5' GNP . . . B 2 -10.997 -11.664 -21.736 1 16.86 ? C5' GNP 167 A 1 HETATM 15 C C4' GNP . . . B 2 -12.167 -10.891 -22.313 1 18.04 ? C4' GNP 167 A 1 HETATM 16 O O4' GNP . . . B 2 -12.105 -11.001 -23.761 1 16.23 ? O4' GNP 167 A 1 HETATM 17 C C3' GNP . . . B 2 -13.541 -11.414 -21.903 1 15.51 ? C3' GNP 167 A 1 HETATM 18 O O3' GNP . . . B 2 -14.443 -10.313 -21.85 1 17.73 ? O3' GNP 167 A 1 HETATM 19 C C2' GNP . . . B 2 -13.873 -12.381 -23.05 1 15.68 ? C2' GNP 167 A 1 HETATM 20 O O2' GNP . . . B 2 -15.241 -12.548 -23.325 1 19.27 ? O2' GNP 167 A 1 HETATM 21 C C1' GNP . . . B 2 -13.278 -11.634 -24.236 1 15.13 ? C1' GNP 167 A 1 HETATM 22 N N9 GNP . . . B 2 -12.889 -12.451 -25.384 1 13.19 ? N9 GNP 167 A 1 HETATM 23 C C8 GNP . . . B 2 -12.021 -13.516 -25.385 1 13.83 ? C8 GNP 167 A 1 HETATM 24 N N7 GNP . . . B 2 -11.835 -14.044 -26.567 1 13.63 ? N7 GNP 167 A 1 HETATM 25 C C5 GNP . . . B 2 -12.623 -13.28 -27.405 1 13.41 ? C5 GNP 167 A 1 HETATM 26 C C6 GNP . . . B 2 -12.803 -13.356 -28.811 1 13.63 ? C6 GNP 167 A 1 HETATM 27 O O6 GNP . . . B 2 -12.288 -14.161 -29.604 1 13.16 ? O6 GNP 167 A 1 HETATM 28 N N1 GNP . . . B 2 -13.664 -12.375 -29.297 1 15.14 ? N1 GNP 167 A 1 HETATM 29 C C2 GNP . . . B 2 -14.278 -11.415 -28.529 1 14.31 ? C2 GNP 167 A 1 HETATM 30 N N2 GNP . . . B 2 -15.081 -10.569 -29.203 1 14.81 ? N2 GNP 167 A 1 HETATM 31 N N3 GNP . . . B 2 -14.112 -11.309 -27.203 1 13.25 ? N3 GNP 167 A 1 HETATM 32 C C4 GNP . . . B 2 -13.27 -12.268 -26.697 1 13.89 ? C4 GNP 167 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 311 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 32 #