data_4S3B # _model_server_result.job_id Il4VDwm0kE63TGbbfPMKXA _model_server_result.datetime_utc '2024-11-13 06:14:14' _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 4s3b # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":901}' # _entry.id 4S3B # _exptl.entry_id 4S3B _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 279.099 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description '(3S)-1,3-dihydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-2-methylbut-2-ylium,carbokation intermediate' _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 127.1 _cell.angle_gamma 90 _cell.entry_id 4S3B _cell.length_a 111.09 _cell.length_b 62.1 _cell.length_c 86.14 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 4S3B _symmetry.cell_setting ? _symmetry.Int_Tables_number 5 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'C 1 2 1' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details dimeric _pdbx_struct_assembly.oligomeric_count 2 _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2 # loop_ _pdbx_struct_oper_list.id _pdbx_struct_oper_list.type _pdbx_struct_oper_list.name _pdbx_struct_oper_list.symmetry_operation _pdbx_struct_oper_list.matrix[1][1] _pdbx_struct_oper_list.matrix[1][2] _pdbx_struct_oper_list.matrix[1][3] _pdbx_struct_oper_list.matrix[2][1] _pdbx_struct_oper_list.matrix[2][2] _pdbx_struct_oper_list.matrix[2][3] _pdbx_struct_oper_list.matrix[3][1] _pdbx_struct_oper_list.matrix[3][2] _pdbx_struct_oper_list.matrix[3][3] _pdbx_struct_oper_list.vector[1] _pdbx_struct_oper_list.vector[2] _pdbx_struct_oper_list.vector[3] 1 'identity operation' 1_555 x,y,z 1 0 0 0 1 0 0 0 1 0 0 0 2 'crystal symmetry operation' 2_555 -x,y,-z -1 0 0 0 1 0 0 0 -1 0 0 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 covale ? covale1 A C ASP 107 A ASP 107 1_555 A N KCX 108 A KCX 108 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.329 ? covale ? covale2 A C KCX 108 A KCX 108 1_555 A N PHE 109 A PHE 109 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.331 ? metalc ? metalc1 A SG CYS 297 A CYS 297 1_555 C FE4 SF4 . A SF4 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.349 ? metalc ? metalc2 A SG CYS 300 A CYS 300 1_555 C FE1 SF4 . A SF4 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.376 ? metalc ? metalc3 A SG CYS 343 A CYS 343 1_555 C FE3 SF4 . A SF4 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.32 ? metalc ? metalc4 B O1 43Q . A 43Q 901 1_555 C FE2 SF4 . A SF4 902 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.946 ? # _chem_comp.formula 'C5 H13 O9 P2 1' _chem_comp.formula_weight 279.099 _chem_comp.id 43Q _chem_comp.mon_nstd_flag . _chem_comp.name '(3S)-1,3-dihydroxy-4-{[(S)-hydroxy(phosphonooxy)phosphoryl]oxy}-2-methylbut-2-ylium, carbokation intermediate' _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 C O 43Q sing 1 n n C C1 43Q sing 2 n n O1 C3 43Q sing 3 n n C1 C3 43Q sing 4 n n C1 C2 43Q sing 5 n n C3 C4 43Q sing 6 n n O4 P1 43Q doub 7 n n C4 O2 43Q sing 8 n n O6 P1 43Q sing 9 n n P1 O3 43Q sing 10 n n P1 O5 43Q sing 11 n n O2 P 43Q sing 12 n n O3 P 43Q sing 13 n n P O8 43Q doub 14 n n P O7 43Q sing 15 n n O6 H1 43Q sing 16 n n O5 H2 43Q sing 17 n n O7 H3 43Q sing 18 n n C4 H4 43Q sing 19 n n C4 H5 43Q sing 20 n n C3 H6 43Q sing 21 n n C H8 43Q sing 22 n n C H9 43Q sing 23 n n O H10 43Q sing 24 n n C2 H11 43Q sing 25 n n C2 H12 43Q sing 26 n n C2 H13 43Q sing 27 n n O1 H14 43Q sing 28 n n # _atom_sites.entry_id 4S3B _atom_sites.fract_transf_matrix[1][1] 0.009002 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.006809 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.016103 _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] 0.014556 _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 43Q A 1 901 901 43Q LIG . C 3 SF4 A 1 902 902 SF4 SF4 . D 4 HOH A 1 1001 1 HOH HOH . D 4 HOH A 2 1002 2 HOH HOH . D 4 HOH A 3 1003 3 HOH HOH . D 4 HOH A 4 1004 4 HOH HOH . D 4 HOH A 5 1005 5 HOH HOH . D 4 HOH A 6 1006 6 HOH HOH . D 4 HOH A 7 1007 7 HOH HOH . D 4 HOH A 8 1008 8 HOH HOH . D 4 HOH A 9 1009 9 HOH HOH . D 4 HOH A 10 1010 10 HOH HOH . D 4 HOH A 11 1011 11 HOH HOH . D 4 HOH A 12 1012 12 HOH HOH . D 4 HOH A 13 1013 13 HOH HOH . D 4 HOH A 14 1014 14 HOH HOH . D 4 HOH A 15 1015 16 HOH HOH . D 4 HOH A 16 1016 17 HOH HOH . D 4 HOH A 17 1017 18 HOH HOH . D 4 HOH A 18 1018 19 HOH HOH . D 4 HOH A 19 1019 20 HOH HOH . D 4 HOH A 20 1020 21 HOH HOH . D 4 HOH A 21 1021 22 HOH HOH . D 4 HOH A 22 1022 23 HOH HOH . D 4 HOH A 23 1023 24 HOH HOH . D 4 HOH A 24 1024 25 HOH HOH . D 4 HOH A 25 1025 26 HOH HOH . D 4 HOH A 26 1026 27 HOH HOH . D 4 HOH A 27 1027 28 HOH HOH . D 4 HOH A 28 1028 29 HOH HOH . D 4 HOH A 29 1029 30 HOH HOH . D 4 HOH A 30 1030 31 HOH HOH . D 4 HOH A 31 1031 32 HOH HOH . D 4 HOH A 32 1032 33 HOH HOH . D 4 HOH A 33 1033 34 HOH HOH . D 4 HOH A 34 1034 35 HOH HOH . D 4 HOH A 35 1035 36 HOH HOH . D 4 HOH A 36 1036 37 HOH HOH . D 4 HOH A 37 1037 38 HOH HOH . D 4 HOH A 38 1038 39 HOH HOH . D 4 HOH A 39 1039 40 HOH HOH . D 4 HOH A 40 1040 41 HOH HOH . D 4 HOH A 41 1041 42 HOH HOH . D 4 HOH A 42 1042 43 HOH HOH . D 4 HOH A 43 1043 44 HOH HOH . D 4 HOH A 44 1044 45 HOH HOH . D 4 HOH A 45 1045 46 HOH HOH . D 4 HOH A 46 1046 47 HOH HOH . D 4 HOH A 47 1047 48 HOH HOH . D 4 HOH A 48 1048 49 HOH HOH . D 4 HOH A 49 1049 50 HOH HOH . D 4 HOH A 50 1050 51 HOH HOH . D 4 HOH A 51 1051 52 HOH HOH . D 4 HOH A 52 1052 53 HOH HOH . D 4 HOH A 53 1053 54 HOH HOH . D 4 HOH A 54 1054 55 HOH HOH . D 4 HOH A 55 1055 56 HOH HOH . D 4 HOH A 56 1056 57 HOH HOH . D 4 HOH A 57 1057 58 HOH HOH . D 4 HOH A 58 1058 59 HOH HOH . D 4 HOH A 59 1059 60 HOH HOH . D 4 HOH A 60 1060 61 HOH HOH . D 4 HOH A 61 1061 62 HOH HOH . D 4 HOH A 62 1062 63 HOH HOH . D 4 HOH A 63 1063 64 HOH HOH . D 4 HOH A 64 1064 65 HOH HOH . D 4 HOH A 65 1065 66 HOH HOH . D 4 HOH A 66 1066 67 HOH HOH . D 4 HOH A 67 1067 68 HOH HOH . D 4 HOH A 68 1068 69 HOH HOH . D 4 HOH A 69 1069 70 HOH HOH . D 4 HOH A 70 1070 71 HOH HOH . D 4 HOH A 71 1071 72 HOH HOH . D 4 HOH A 72 1072 73 HOH HOH . D 4 HOH A 73 1073 74 HOH HOH . D 4 HOH A 74 1074 75 HOH HOH . D 4 HOH A 75 1075 76 HOH HOH . D 4 HOH A 76 1076 77 HOH HOH . D 4 HOH A 77 1077 78 HOH HOH . D 4 HOH A 78 1078 79 HOH HOH . D 4 HOH A 79 1079 80 HOH HOH . D 4 HOH A 80 1080 81 HOH HOH . D 4 HOH A 81 1081 82 HOH HOH . D 4 HOH A 82 1082 83 HOH HOH . D 4 HOH A 83 1083 84 HOH HOH . D 4 HOH A 84 1084 85 HOH HOH . D 4 HOH A 85 1085 86 HOH HOH . D 4 HOH A 86 1086 87 HOH HOH . D 4 HOH A 87 1087 88 HOH HOH . D 4 HOH A 88 1088 89 HOH HOH . D 4 HOH A 89 1089 90 HOH HOH . D 4 HOH A 90 1090 91 HOH HOH . D 4 HOH A 91 1091 92 HOH HOH . D 4 HOH A 92 1092 93 HOH HOH . D 4 HOH A 93 1093 94 HOH HOH . D 4 HOH A 94 1094 95 HOH HOH . D 4 HOH A 95 1095 96 HOH HOH . D 4 HOH A 96 1096 97 HOH HOH . D 4 HOH A 97 1097 98 HOH HOH . D 4 HOH A 98 1098 99 HOH HOH . D 4 HOH A 99 1099 100 HOH HOH . D 4 HOH A 100 1100 101 HOH HOH . D 4 HOH A 101 1101 102 HOH HOH . D 4 HOH A 102 1102 103 HOH HOH . D 4 HOH A 103 1103 105 HOH HOH . D 4 HOH A 104 1104 106 HOH HOH . D 4 HOH A 105 1105 107 HOH HOH . D 4 HOH A 106 1106 108 HOH HOH . D 4 HOH A 107 1107 109 HOH HOH . D 4 HOH A 108 1108 110 HOH HOH . D 4 HOH A 109 1109 111 HOH HOH . D 4 HOH A 110 1110 112 HOH HOH . D 4 HOH A 111 1111 113 HOH HOH . D 4 HOH A 112 1112 114 HOH HOH . D 4 HOH A 113 1113 115 HOH HOH . D 4 HOH A 114 1114 116 HOH HOH . D 4 HOH A 115 1115 117 HOH HOH . D 4 HOH A 116 1116 118 HOH HOH . D 4 HOH A 117 1117 119 HOH HOH . D 4 HOH A 118 1118 120 HOH HOH . D 4 HOH A 119 1119 121 HOH HOH . D 4 HOH A 120 1120 122 HOH HOH . D 4 HOH A 121 1121 123 HOH HOH . D 4 HOH A 122 1122 124 HOH HOH . D 4 HOH A 123 1123 125 HOH HOH . D 4 HOH A 124 1124 126 HOH HOH . D 4 HOH A 125 1125 127 HOH HOH . D 4 HOH A 126 1126 128 HOH HOH . D 4 HOH A 127 1127 129 HOH HOH . D 4 HOH A 128 1128 131 HOH HOH . D 4 HOH A 129 1129 132 HOH HOH . D 4 HOH A 130 1130 133 HOH HOH . D 4 HOH A 131 1131 134 HOH HOH . D 4 HOH A 132 1132 135 HOH HOH . D 4 HOH A 133 1133 136 HOH HOH . D 4 HOH A 134 1134 137 HOH HOH . D 4 HOH A 135 1135 138 HOH HOH . D 4 HOH A 136 1136 139 HOH HOH . D 4 HOH A 137 1137 140 HOH HOH . D 4 HOH A 138 1138 141 HOH HOH . D 4 HOH A 139 1139 142 HOH HOH . D 4 HOH A 140 1140 143 HOH HOH . D 4 HOH A 141 1141 145 HOH HOH . D 4 HOH A 142 1142 146 HOH HOH . D 4 HOH A 143 1143 147 HOH HOH . D 4 HOH A 144 1144 148 HOH HOH . D 4 HOH A 145 1145 149 HOH HOH . D 4 HOH A 146 1146 150 HOH HOH . D 4 HOH A 147 1147 151 HOH HOH . D 4 HOH A 148 1148 152 HOH HOH . D 4 HOH A 149 1149 153 HOH HOH . D 4 HOH A 150 1150 154 HOH HOH . D 4 HOH A 151 1151 155 HOH HOH . D 4 HOH A 152 1152 156 HOH HOH . D 4 HOH A 153 1153 157 HOH HOH . D 4 HOH A 154 1154 158 HOH HOH . D 4 HOH A 155 1155 159 HOH HOH . D 4 HOH A 156 1156 160 HOH HOH . D 4 HOH A 157 1157 161 HOH HOH . D 4 HOH A 158 1158 162 HOH HOH . D 4 HOH A 159 1159 163 HOH HOH . D 4 HOH A 160 1160 164 HOH HOH . D 4 HOH A 161 1161 165 HOH HOH . D 4 HOH A 162 1162 166 HOH HOH . D 4 HOH A 163 1163 167 HOH HOH . D 4 HOH A 164 1164 168 HOH HOH . D 4 HOH A 165 1165 169 HOH HOH . D 4 HOH A 166 1166 170 HOH HOH . D 4 HOH A 167 1167 171 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 O O6 43Q . . . B 2 13.37 22.98 -15.475 1 24.93 ? O6 43Q 901 A 1 HETATM 2 P P1 43Q . . . B 2 12.477 21.98 -14.931 1 23.64 ? P1 43Q 901 A 1 HETATM 3 O O5 43Q . . . B 2 13.178 21.207 -13.771 1 26.77 ? O5 43Q 901 A 1 HETATM 4 O O4 43Q . . . B 2 12.085 20.97 -16.065 1 24.29 ? O4 43Q 901 A 1 HETATM 5 O O3 43Q . . . B 2 11.118 22.673 -14.463 1 22.77 ? O3 43Q 901 A 1 HETATM 6 P P 43Q . . . B 2 10.995 24.01 -13.601 1 23.91 ? P 43Q 901 A 1 HETATM 7 O O8 43Q . . . B 2 9.571 24.11 -13.252 1 22.28 ? O8 43Q 901 A 1 HETATM 8 O O7 43Q . . . B 2 11.946 23.983 -12.392 1 26.07 ? O7 43Q 901 A 1 HETATM 9 O O2 43Q . . . B 2 11.49 25.253 -14.519 1 28.28 ? O2 43Q 901 A 1 HETATM 10 C C4 43Q . . . B 2 10.728 25.808 -15.62 1 28.09 ? C4 43Q 901 A 1 HETATM 11 C C3 43Q . . . B 2 11.085 25.356 -17.076 1 29.17 ? C3 43Q 901 A 1 HETATM 12 C C1 43Q . . . B 2 12.518 25.58 -17.605 1 28.63 ? C1 43Q 901 A 1 HETATM 13 C C 43Q . . . B 2 13.185 24.363 -18.253 1 27.96 ? C 43Q 901 A 1 HETATM 14 O O 43Q . . . B 2 12.369 23.177 -18.426 1 32.77 ? O 43Q 901 A 1 HETATM 15 C C2 43Q . . . B 2 13.458 26.304 -16.646 1 23.75 ? C2 43Q 901 A 1 HETATM 16 O O1 43Q . . . B 2 10.273 26.055 -18.113 1 34.26 ? O1 43Q 901 A 1 # _model_server_stats.io_time_ms 13 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 267 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 16 #