data_2QQF # _model_server_result.job_id b3YAFXwOHm7vpUggvVJQtA _model_server_result.datetime_utc '2024-11-15 04:14:26' _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 2qqf # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1001}' # _entry.id 2QQF # _exptl.entry_id 2QQF _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 542.332 _entity.id 4 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE" _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 2QQF _cell.length_a 105.94 _cell.length_b 105.94 _cell.length_c 67.1 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2QQF _symmetry.cell_setting ? _symmetry.Int_Tables_number 154 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 32 2 1' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PISA tetrameric 4 software_defined_assembly 1 ? dimeric 2 author_defined_assembly 2 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,B,C,D,E,F 1 1,2 A,B,C,D,E,F 2 1 # 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' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 67.1 # _struct_asym.details ? _struct_asym.entity_id 4 _struct_asym.id D _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 B C ALA 4 B ALA 15 1_555 B N ALY 5 B ALY 16 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.332 ? covale ? covale2 B C ALY 5 B ALY 16 1_555 B N ARG 6 B ARG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.33 ? metalc ? metalc1 A SG CYS 157 A CYS 143 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.476 ? metalc ? metalc2 A SG CYS 160 A CYS 146 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.432 ? metalc ? metalc3 A SG CYS 184 A CYS 170 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.368 ? metalc ? metalc4 A SG CYS 187 A CYS 173 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.455 ? # _chem_comp.formula 'C15 H24 N6 O12 P2' _chem_comp.formula_weight 542.332 _chem_comp.id A1R _chem_comp.mon_nstd_flag . _chem_comp.name "5'-O-[(S)-{[(S)-{[(2R,3R,4S)-3,4-DIHYDROXYPYRROLIDIN-2-YL]METHOXY}(HYDROXY)PHOSPHORYL]OXY}(HYDROXY)PHOSPHORYL]ADENOSINE" _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 N1 C2 A1R doub 1 n y N1 C6 A1R sing 2 n y C2 N3 A1R sing 3 n y C2 H2 A1R sing 4 n n N3 C4 A1R doub 5 n y C4 C5 A1R sing 6 n y C4 N9 A1R sing 7 n y C5 C6 A1R doub 8 n y C5 N7 A1R sing 9 n y C6 N6 A1R sing 10 n n N6 HN61 A1R sing 11 n n N6 HN62 A1R sing 12 n n N7 C8 A1R doub 13 n y C8 N9 A1R sing 14 n y C8 H8 A1R sing 15 n n N9 C1' A1R sing 16 n n C1' O4' A1R sing 17 n n C1' C2' A1R sing 18 n n C1' H1' A1R sing 19 n n C2' O2' A1R sing 20 n n C2' C3' A1R sing 21 n n C2' H2' A1R sing 22 n n O2' HO2' A1R sing 23 n n C3' C4' A1R sing 24 n n C3' O3' A1R sing 25 n n C3' H3' A1R sing 26 n n O3' HO3' A1R sing 27 n n O4' C4' A1R sing 28 n n C4' C5' A1R sing 29 n n C4' H4' A1R sing 30 n n C5' O5' A1R sing 31 n n C5' "H5'1" A1R sing 32 n n C5' "H5'2" A1R sing 33 n n O5' PA A1R sing 34 n n PA O3A A1R sing 35 n n PA O1A A1R doub 36 n n PA O2A A1R sing 37 n n O2A HO2A A1R sing 38 n n O3A PB A1R sing 39 n n PB O2B A1R doub 40 n n PB O1B A1R sing 41 n n PB O5N A1R sing 42 n n O1B HO1B A1R sing 43 n n O5N C5N A1R sing 44 n n C5N C4N A1R sing 45 n n C5N H5N1 A1R sing 46 n n C5N H5N2 A1R sing 47 n n N4N C4N A1R sing 48 n n N4N C1N A1R sing 49 n n N4N HN4N A1R sing 50 n n C1N C2N A1R sing 51 n n C1N H1N1 A1R sing 52 n n C1N H1N2 A1R sing 53 n n O2N C2N A1R sing 54 n n O2N HO2N A1R sing 55 n n C2N C3N A1R sing 56 n n C2N H2N A1R sing 57 n n O3N C3N A1R sing 58 n n O3N HO3N A1R sing 59 n n C3N C4N A1R sing 60 n n C3N H3N A1R sing 61 n n C4N H4N A1R sing 62 n n # _atom_sites.entry_id 2QQF _atom_sites.fract_transf_matrix[1][1] 0.009439 _atom_sites.fract_transf_matrix[1][2] 0.00545 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.0109 _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] 0.014903 _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 C 3 ZN A 1 701 701 ZN ZN . D 4 A1R A 1 1001 1001 A1R A1R . E 5 HOH A 1 1002 1002 HOH HOH . E 5 HOH A 2 1003 1003 HOH HOH . E 5 HOH A 3 1004 1004 HOH HOH . E 5 HOH A 4 1005 1005 HOH HOH . E 5 HOH A 5 1006 1006 HOH HOH . E 5 HOH A 6 1007 1007 HOH HOH . E 5 HOH A 7 1008 1008 HOH HOH . E 5 HOH A 8 1009 1009 HOH HOH . E 5 HOH A 9 1010 1010 HOH HOH . E 5 HOH A 10 1011 1011 HOH HOH . E 5 HOH A 11 1012 1012 HOH HOH . E 5 HOH A 12 1013 1013 HOH HOH . E 5 HOH A 13 1014 1014 HOH HOH . E 5 HOH A 14 1015 1015 HOH HOH . E 5 HOH A 15 1016 1016 HOH HOH . E 5 HOH A 16 1017 1017 HOH HOH . E 5 HOH A 17 1018 1018 HOH HOH . E 5 HOH A 18 1019 1019 HOH HOH . E 5 HOH A 19 1020 1020 HOH HOH . E 5 HOH A 20 1021 1021 HOH HOH . E 5 HOH A 21 1022 1022 HOH HOH . E 5 HOH A 22 1023 1023 HOH HOH . E 5 HOH A 23 1024 1024 HOH HOH . E 5 HOH A 24 1025 1025 HOH HOH . E 5 HOH A 25 1026 1026 HOH HOH . E 5 HOH A 26 1027 1027 HOH HOH . E 5 HOH A 27 1028 1028 HOH HOH . E 5 HOH A 28 1029 1029 HOH HOH . E 5 HOH A 29 1030 1030 HOH HOH . E 5 HOH A 30 1031 1031 HOH HOH . E 5 HOH A 31 1032 1032 HOH HOH . E 5 HOH A 32 1033 1033 HOH HOH . E 5 HOH A 33 1034 1034 HOH HOH . E 5 HOH A 34 1035 1035 HOH HOH . E 5 HOH A 35 1036 1036 HOH HOH . E 5 HOH A 36 1037 1037 HOH HOH . E 5 HOH A 37 1038 1038 HOH HOH . E 5 HOH A 38 1039 1039 HOH HOH . E 5 HOH A 39 1040 1040 HOH HOH . E 5 HOH A 40 1041 1041 HOH HOH . E 5 HOH A 41 1042 1042 HOH HOH . E 5 HOH A 42 1043 1043 HOH HOH . E 5 HOH A 43 1044 1044 HOH HOH . E 5 HOH A 44 1045 1045 HOH HOH . E 5 HOH A 45 1046 1046 HOH HOH . E 5 HOH A 46 1047 1047 HOH HOH . E 5 HOH A 47 1048 1048 HOH HOH . E 5 HOH A 48 1049 1049 HOH HOH . E 5 HOH A 49 1050 1050 HOH HOH . E 5 HOH A 50 1051 1051 HOH HOH . E 5 HOH A 51 1052 1052 HOH HOH . E 5 HOH A 52 1053 1053 HOH HOH . E 5 HOH A 53 1054 1054 HOH HOH . E 5 HOH A 54 1055 1055 HOH HOH . E 5 HOH A 55 1056 1056 HOH HOH . E 5 HOH A 56 1057 1057 HOH HOH . E 5 HOH A 57 1058 1058 HOH HOH . E 5 HOH A 58 1059 1059 HOH HOH . E 5 HOH A 59 1060 1060 HOH HOH . E 5 HOH A 60 1061 1061 HOH HOH . E 5 HOH A 61 1062 1062 HOH HOH . E 5 HOH A 62 1063 1063 HOH HOH . E 5 HOH A 63 1064 1064 HOH HOH . E 5 HOH A 64 1065 1065 HOH HOH . E 5 HOH A 65 1066 1066 HOH HOH . E 5 HOH A 66 1067 1067 HOH HOH . E 5 HOH A 67 1068 1068 HOH HOH . E 5 HOH A 68 1069 1069 HOH HOH . E 5 HOH A 69 1070 1070 HOH HOH . E 5 HOH A 70 1071 1071 HOH HOH . E 5 HOH A 71 1072 1072 HOH HOH . E 5 HOH A 72 1073 1073 HOH HOH . E 5 HOH A 73 1074 1074 HOH HOH . E 5 HOH A 74 1075 1075 HOH HOH . E 5 HOH A 75 1076 1076 HOH HOH . E 5 HOH A 76 1077 1077 HOH HOH . E 5 HOH A 77 1078 1078 HOH HOH . E 5 HOH A 78 1079 1079 HOH HOH . E 5 HOH A 79 1080 1080 HOH HOH . E 5 HOH A 80 1081 1081 HOH HOH . E 5 HOH A 81 1082 1082 HOH HOH . E 5 HOH A 82 1083 1083 HOH HOH . E 5 HOH A 83 1084 1084 HOH HOH . E 5 HOH A 84 1085 1085 HOH HOH . E 5 HOH A 85 1086 1086 HOH HOH . E 5 HOH A 86 1087 1087 HOH HOH . E 5 HOH A 87 1088 1088 HOH HOH . E 5 HOH A 88 1089 1089 HOH HOH . E 5 HOH A 89 1090 1090 HOH HOH . E 5 HOH A 90 1091 1091 HOH HOH . E 5 HOH A 91 1092 1092 HOH HOH . E 5 HOH A 92 1093 1093 HOH HOH . E 5 HOH A 93 1094 1094 HOH HOH . E 5 HOH A 94 1095 1095 HOH HOH . E 5 HOH A 95 1096 1096 HOH HOH . E 5 HOH A 96 1097 1097 HOH HOH . E 5 HOH A 97 1098 1098 HOH HOH . E 5 HOH A 98 1099 1099 HOH HOH . E 5 HOH A 99 1100 1100 HOH HOH . E 5 HOH A 100 1101 1101 HOH HOH . E 5 HOH A 101 1102 1102 HOH HOH . E 5 HOH A 102 1103 1103 HOH HOH . E 5 HOH A 103 1104 1104 HOH HOH . E 5 HOH A 104 1105 1105 HOH HOH . E 5 HOH A 105 1106 1106 HOH HOH . E 5 HOH A 106 1107 1107 HOH HOH . E 5 HOH A 107 1108 1108 HOH HOH . E 5 HOH A 108 1109 1109 HOH HOH . E 5 HOH A 109 1110 1110 HOH HOH . E 5 HOH A 110 1111 1111 HOH HOH . E 5 HOH A 111 1112 1112 HOH HOH . E 5 HOH A 112 1113 1113 HOH HOH . E 5 HOH A 113 1114 1114 HOH HOH . E 5 HOH A 114 1115 1115 HOH HOH . E 5 HOH A 115 1116 1116 HOH HOH . E 5 HOH A 116 1117 1117 HOH HOH . E 5 HOH A 117 1118 1118 HOH HOH . E 5 HOH A 118 1119 1119 HOH HOH . E 5 HOH A 119 1120 1120 HOH HOH . E 5 HOH A 120 1121 1121 HOH HOH . E 5 HOH A 121 1122 1122 HOH HOH . E 5 HOH A 122 1123 1123 HOH HOH . E 5 HOH A 123 1124 1124 HOH HOH . E 5 HOH A 124 1125 1125 HOH HOH . E 5 HOH A 125 1126 1126 HOH HOH . E 5 HOH A 126 1127 1127 HOH HOH . E 5 HOH A 127 1128 1128 HOH HOH . E 5 HOH A 128 1129 1129 HOH HOH . E 5 HOH A 129 1130 1130 HOH HOH . E 5 HOH A 130 1131 1131 HOH HOH . E 5 HOH A 131 1132 1132 HOH HOH . E 5 HOH A 132 1133 1133 HOH HOH . F 5 HOH B 1 49 49 HOH HOH . F 5 HOH B 2 50 134 HOH HOH . F 5 HOH B 3 51 135 HOH HOH . F 5 HOH B 4 52 137 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 N N1 A1R . . . D 4 39.606 59.106 23.715 1 31.4 ? N1 A1R 1001 A 1 HETATM 2 C C2 A1R . . . D 4 40.64 60.066 23.955 1 32.69 ? C2 A1R 1001 A 1 HETATM 3 N N3 A1R . . . D 4 40.945 60.568 25.306 1 33.47 ? N3 A1R 1001 A 1 HETATM 4 C C4 A1R . . . D 4 40.103 60.003 26.363 1 33.44 ? C4 A1R 1001 A 1 HETATM 5 C C5 A1R . . . D 4 39.055 59.052 26.237 1 32.64 ? C5 A1R 1001 A 1 HETATM 6 C C6 A1R . . . D 4 38.803 58.584 24.819 1 31.73 ? C6 A1R 1001 A 1 HETATM 7 N N6 A1R . . . D 4 37.802 57.638 24.488 1 29.71 ? N6 A1R 1001 A 1 HETATM 8 N N7 A1R . . . D 4 38.498 58.772 27.473 1 34.15 ? N7 A1R 1001 A 1 HETATM 9 C C8 A1R . . . D 4 39.178 59.52 28.348 1 34.2 ? C8 A1R 1001 A 1 HETATM 10 N N9 A1R . . . D 4 40.169 60.288 27.724 1 33.66 ? N9 A1R 1001 A 1 HETATM 11 C C1' A1R . . . D 4 41.162 61.248 28.255 1 33.69 ? C1' A1R 1001 A 1 HETATM 12 C C2' A1R . . . D 4 40.837 62.171 29.354 1 33.37 ? C2' A1R 1001 A 1 HETATM 13 O O2' A1R . . . D 4 40.636 63.526 28.869 1 33.61 ? O2' A1R 1001 A 1 HETATM 14 C C3' A1R . . . D 4 41.956 62.047 30.332 1 33.06 ? C3' A1R 1001 A 1 HETATM 15 O O3' A1R . . . D 4 42.805 63.22 30.484 1 33.9 ? O3' A1R 1001 A 1 HETATM 16 O O4' A1R . . . D 4 42.244 60.448 28.638 1 32.7 ? O4' A1R 1001 A 1 HETATM 17 C C4' A1R . . . D 4 42.791 60.851 29.903 1 33.17 ? C4' A1R 1001 A 1 HETATM 18 C C5' A1R . . . D 4 42.733 59.579 30.829 1 33.53 ? C5' A1R 1001 A 1 HETATM 19 O O5' A1R . . . D 4 43.26 59.911 32.152 1 35.04 ? O5' A1R 1001 A 1 HETATM 20 P PA A1R . . . D 4 43.359 58.909 33.324 1 35.15 ? PA A1R 1001 A 1 HETATM 21 O O1A A1R . . . D 4 42.074 58.267 33.663 1 35.59 ? O1A A1R 1001 A 1 HETATM 22 O O2A A1R . . . D 4 43.917 59.644 34.469 1 32.75 ? O2A A1R 1001 A 1 HETATM 23 O O3A A1R . . . D 4 44.45 57.842 33.125 1 38.06 ? O3A A1R 1001 A 1 HETATM 24 P PB A1R . . . D 4 45.902 57.668 32.766 1 40.39 ? PB A1R 1001 A 1 HETATM 25 O O1B A1R . . . D 4 46.556 58.944 32.459 1 40.78 ? O1B A1R 1001 A 1 HETATM 26 O O2B A1R . . . D 4 46.245 56.921 31.634 1 44.07 ? O2B A1R 1001 A 1 HETATM 27 O O5N A1R . . . D 4 46.35 57.328 34.184 1 43.04 ? O5N A1R 1001 A 1 HETATM 28 C C5N A1R . . . D 4 46.138 56.35 35.081 1 46.02 ? C5N A1R 1001 A 1 HETATM 29 N N4N A1R . . . D 4 44.741 55.526 36.517 1 49.97 ? N4N A1R 1001 A 1 HETATM 30 C C1N A1R . . . D 4 45.066 55.071 37.897 1 49.72 ? C1N A1R 1001 A 1 HETATM 31 O O2N A1R . . . D 4 44.922 56.598 39.209 1 52.79 ? O2N A1R 1001 A 1 HETATM 32 C C2N A1R . . . D 4 45.98 55.931 38.434 1 50.67 ? C2N A1R 1001 A 1 HETATM 33 O O3N A1R . . . D 4 46.422 58.394 37.878 1 52.06 ? O3N A1R 1001 A 1 HETATM 34 C C3N A1R . . . D 4 46.376 57.007 37.567 1 50.11 ? C3N A1R 1001 A 1 HETATM 35 C C4N A1R . . . D 4 45.565 56.768 36.297 1 48.76 ? C4N A1R 1001 A 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 12 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 315 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 35 #