data_2D4N # _model_server_result.job_id uMa2Qr5sijYQzQIol4t7YA _model_server_result.datetime_utc '2024-11-27 00:59:06' _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 2d4n # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":777}' # _entry.id 2D4N # _exptl.entry_id 2D4N _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 467.157 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _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 2D4N _cell.length_a 61.071 _cell.length_b 61.071 _cell.length_c 64.357 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2D4N _symmetry.cell_setting ? _symmetry.Int_Tables_number 173 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 63' # _pdbx_struct_assembly.method_details PISA,PQS _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 _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 1,2,3 # 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_775 -y+2,x-y+2,z -0.5 -0.866025 0 0.866025 -0.5 0 0 0 1 61.071 105.778075 0 3 'crystal symmetry operation' 3_575 -x+y,-x+2,z -0.5 0.866025 0 -0.866025 -0.5 0 0 0 1 -61.071 105.778075 0 # _struct_asym.details ? _struct_asym.entity_id 3 _struct_asym.id C _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 C O2G DUP . A DUP 777 1_555 B MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.988 ? metalc ? metalc2 C O1B DUP . A DUP 777 1_555 B MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.05 ? metalc ? metalc3 C O1A DUP . A DUP 777 1_555 B MG MG . A MG 999 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.094 ? metalc ? metalc4 B MG MG . A MG 999 1_555 E O HOH . A HOH 1127 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.036 ? metalc ? metalc5 B MG MG . A MG 999 1_555 E O HOH . A HOH 1128 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.124 ? metalc ? metalc6 B MG MG . A MG 999 1_555 E O HOH . A HOH 1130 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.121 ? # _chem_comp.formula 'C9 H16 N3 O13 P3' _chem_comp.formula_weight 467.157 _chem_comp.id DUP _chem_comp.mon_nstd_flag . _chem_comp.name "2'-DEOXYURIDINE 5'-ALPHA,BETA-IMIDO-TRIPHOSPHATE" _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 O4 C4 DUP doub 83 n n C4 C5 DUP sing 84 n y C4 N3 DUP sing 85 n y C5 C6 DUP doub 86 n y C5 H5 DUP sing 87 n n C6 N1 DUP sing 88 n y C6 H6 DUP sing 89 n n N3 C2 DUP sing 90 n y N3 HN3 DUP sing 91 n n C2 O2 DUP doub 92 n n C2 N1 DUP sing 93 n y N1 C1' DUP sing 94 n n C1' C2' DUP sing 95 n n C1' O4' DUP sing 96 n n C1' H1' DUP sing 97 n n C2' C3' DUP sing 98 n n C2' "H2'1" DUP sing 99 n n C2' "H2'2" DUP sing 100 n n C3' O3' DUP sing 101 n n C3' C4' DUP sing 102 n n C3' H1 DUP sing 103 n n O3' H3' DUP sing 104 n n O4' C4' DUP sing 105 n n C4' C5' DUP sing 106 n n C4' H4' DUP sing 107 n n C5' O5' DUP sing 108 n n C5' "H5'1" DUP sing 109 n n C5' "H5'2" DUP sing 110 n n O5' PA DUP sing 111 n n PA O1A DUP doub 112 n n PA O2A DUP sing 113 n n PA N3A DUP sing 114 n n O2A H2A DUP sing 115 n n N3A PB DUP sing 116 n n N3A H3A DUP sing 117 n n PB O1B DUP doub 118 n n PB O2B DUP sing 119 n n PB O3B DUP sing 120 n n O2B H2B DUP sing 121 n n O3B PG DUP sing 122 n n PG O2G DUP doub 123 n n PG O1G DUP sing 124 n n PG O3G DUP sing 125 n n O1G H1G DUP sing 126 n n O3G H3G DUP sing 127 n n # _atom_sites.entry_id 2D4N _atom_sites.fract_transf_matrix[1][1] 0.016374 _atom_sites.fract_transf_matrix[1][2] 0.009454 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.018908 _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] 0.015538 _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 MG A 1 999 999 MG MG . C 3 DUP A 1 777 777 DUP UNP . D 4 TRS A 1 1001 1 TRS TRS . E 5 HOH A 1 1002 1 HOH HOH . E 5 HOH A 2 1003 2 HOH HOH . E 5 HOH A 3 1004 3 HOH HOH . E 5 HOH A 4 1005 4 HOH HOH . E 5 HOH A 5 1006 5 HOH HOH . E 5 HOH A 6 1007 6 HOH HOH . E 5 HOH A 7 1008 8 HOH HOH . E 5 HOH A 8 1009 9 HOH HOH . E 5 HOH A 9 1010 10 HOH HOH . E 5 HOH A 10 1011 11 HOH HOH . E 5 HOH A 11 1012 12 HOH HOH . E 5 HOH A 12 1013 13 HOH HOH . E 5 HOH A 13 1014 15 HOH HOH . E 5 HOH A 14 1015 16 HOH HOH . E 5 HOH A 15 1016 17 HOH HOH . E 5 HOH A 16 1017 18 HOH HOH . E 5 HOH A 17 1018 19 HOH HOH . E 5 HOH A 18 1019 20 HOH HOH . E 5 HOH A 19 1020 21 HOH HOH . E 5 HOH A 20 1021 22 HOH HOH . E 5 HOH A 21 1022 23 HOH HOH . E 5 HOH A 22 1023 24 HOH HOH . E 5 HOH A 23 1024 25 HOH HOH . E 5 HOH A 24 1025 26 HOH HOH . E 5 HOH A 25 1026 27 HOH HOH . E 5 HOH A 26 1027 28 HOH HOH . E 5 HOH A 27 1028 29 HOH HOH . E 5 HOH A 28 1029 30 HOH HOH . E 5 HOH A 29 1030 31 HOH HOH . E 5 HOH A 30 1031 32 HOH HOH . E 5 HOH A 31 1032 33 HOH HOH . E 5 HOH A 32 1033 34 HOH HOH . E 5 HOH A 33 1034 35 HOH HOH . E 5 HOH A 34 1035 36 HOH HOH . E 5 HOH A 35 1036 37 HOH HOH . E 5 HOH A 36 1037 38 HOH HOH . E 5 HOH A 37 1038 39 HOH HOH . E 5 HOH A 38 1039 40 HOH HOH . E 5 HOH A 39 1040 42 HOH HOH . E 5 HOH A 40 1041 43 HOH HOH . E 5 HOH A 41 1042 44 HOH HOH . E 5 HOH A 42 1043 45 HOH HOH . E 5 HOH A 43 1044 46 HOH HOH . E 5 HOH A 44 1045 47 HOH HOH . E 5 HOH A 45 1046 48 HOH HOH . E 5 HOH A 46 1047 49 HOH HOH . E 5 HOH A 47 1048 50 HOH HOH . E 5 HOH A 48 1049 51 HOH HOH . E 5 HOH A 49 1050 52 HOH HOH . E 5 HOH A 50 1051 53 HOH HOH . E 5 HOH A 51 1052 54 HOH HOH . E 5 HOH A 52 1053 55 HOH HOH . E 5 HOH A 53 1054 56 HOH HOH . E 5 HOH A 54 1055 57 HOH HOH . E 5 HOH A 55 1056 58 HOH HOH . E 5 HOH A 56 1057 59 HOH HOH . E 5 HOH A 57 1058 60 HOH HOH . E 5 HOH A 58 1059 61 HOH HOH . E 5 HOH A 59 1060 62 HOH HOH . E 5 HOH A 60 1061 63 HOH HOH . E 5 HOH A 61 1062 64 HOH HOH . E 5 HOH A 62 1063 65 HOH HOH . E 5 HOH A 63 1064 66 HOH HOH . E 5 HOH A 64 1065 67 HOH HOH . E 5 HOH A 65 1066 68 HOH HOH . E 5 HOH A 66 1067 69 HOH HOH . E 5 HOH A 67 1068 70 HOH HOH . E 5 HOH A 68 1069 71 HOH HOH . E 5 HOH A 69 1070 72 HOH HOH . E 5 HOH A 70 1071 73 HOH HOH . E 5 HOH A 71 1072 74 HOH HOH . E 5 HOH A 72 1073 75 HOH HOH . E 5 HOH A 73 1074 76 HOH HOH . E 5 HOH A 74 1075 77 HOH HOH . E 5 HOH A 75 1076 78 HOH HOH . E 5 HOH A 76 1077 79 HOH HOH . E 5 HOH A 77 1078 80 HOH HOH . E 5 HOH A 78 1079 81 HOH HOH . E 5 HOH A 79 1080 82 HOH HOH . E 5 HOH A 80 1081 83 HOH HOH . E 5 HOH A 81 1082 84 HOH HOH . E 5 HOH A 82 1083 85 HOH HOH . E 5 HOH A 83 1084 86 HOH HOH . E 5 HOH A 84 1085 87 HOH HOH . E 5 HOH A 85 1086 88 HOH HOH . E 5 HOH A 86 1087 89 HOH HOH . E 5 HOH A 87 1088 90 HOH HOH . E 5 HOH A 88 1089 91 HOH HOH . E 5 HOH A 89 1090 92 HOH HOH . E 5 HOH A 90 1091 93 HOH HOH . E 5 HOH A 91 1092 94 HOH HOH . E 5 HOH A 92 1093 95 HOH HOH . E 5 HOH A 93 1094 96 HOH HOH . E 5 HOH A 94 1095 97 HOH HOH . E 5 HOH A 95 1096 98 HOH HOH . E 5 HOH A 96 1097 99 HOH HOH . E 5 HOH A 97 1098 100 HOH HOH . E 5 HOH A 98 1099 101 HOH HOH . E 5 HOH A 99 1100 102 HOH HOH . E 5 HOH A 100 1101 103 HOH HOH . E 5 HOH A 101 1102 104 HOH HOH . E 5 HOH A 102 1103 105 HOH HOH . E 5 HOH A 103 1104 106 HOH HOH . E 5 HOH A 104 1105 107 HOH HOH . E 5 HOH A 105 1106 108 HOH HOH . E 5 HOH A 106 1107 109 HOH HOH . E 5 HOH A 107 1108 111 HOH HOH . E 5 HOH A 108 1109 112 HOH HOH . E 5 HOH A 109 1110 113 HOH HOH . E 5 HOH A 110 1111 114 HOH HOH . E 5 HOH A 111 1112 115 HOH HOH . E 5 HOH A 112 1113 116 HOH HOH . E 5 HOH A 113 1114 118 HOH HOH . E 5 HOH A 114 1115 120 HOH HOH . E 5 HOH A 115 1116 121 HOH HOH . E 5 HOH A 116 1117 122 HOH HOH . E 5 HOH A 117 1118 125 HOH HOH . E 5 HOH A 118 1119 126 HOH HOH . E 5 HOH A 119 1120 127 HOH HOH . E 5 HOH A 120 1121 128 HOH HOH . E 5 HOH A 121 1122 129 HOH HOH . E 5 HOH A 122 1123 130 HOH HOH . E 5 HOH A 123 1124 131 HOH HOH . E 5 HOH A 124 1125 132 HOH HOH . E 5 HOH A 125 1126 133 HOH HOH . E 5 HOH A 126 1127 134 HOH HOH . E 5 HOH A 127 1128 135 HOH HOH . E 5 HOH A 128 1129 136 HOH HOH . E 5 HOH A 129 1130 137 HOH HOH . E 5 HOH A 130 1131 138 HOH HOH . E 5 HOH A 131 1132 139 HOH HOH . E 5 HOH A 132 1133 140 HOH HOH . E 5 HOH A 133 1134 141 HOH HOH . E 5 HOH A 134 1135 142 HOH HOH . E 5 HOH A 135 1136 143 HOH HOH . E 5 HOH A 136 1137 144 HOH HOH . E 5 HOH A 137 1138 145 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 O4 DUP . . . C 3 -2.556 60.262 29.149 1 16.36 ? O4 DUP 777 A 1 HETATM 2 C C4 DUP . . . C 3 -3.418 59.641 29.768 1 14.79 ? C4 DUP 777 A 1 HETATM 3 C C5 DUP . . . C 3 -4.636 60.16 30.182 1 14.11 ? C5 DUP 777 A 1 HETATM 4 C C6 DUP . . . C 3 -5.531 59.329 30.842 1 14.61 ? C6 DUP 777 A 1 HETATM 5 N N3 DUP . . . C 3 -3.155 58.308 29.92 1 14.7 ? N3 DUP 777 A 1 HETATM 6 C C2 DUP . . . C 3 -4.073 57.499 30.557 1 14.83 ? C2 DUP 777 A 1 HETATM 7 O O2 DUP . . . C 3 -3.761 56.297 30.756 1 15.26 ? O2 DUP 777 A 1 HETATM 8 N N1 DUP . . . C 3 -5.225 58.011 31.059 1 14.72 ? N1 DUP 777 A 1 HETATM 9 C C1' DUP . . . C 3 -6.176 57.119 31.799 1 14.1 ? C1' DUP 777 A 1 HETATM 10 C C2' DUP . . . C 3 -5.95 57.315 33.308 1 16.4 ? C2' DUP 777 A 1 HETATM 11 C C3' DUP . . . C 3 -7.136 58.172 33.755 1 15.7 ? C3' DUP 777 A 1 HETATM 12 O O3' DUP . . . C 3 -7.534 58.007 35.103 1 16.59 ? O3' DUP 777 A 1 HETATM 13 O O4' DUP . . . C 3 -7.493 57.52 31.524 1 16.63 ? O4' DUP 777 A 1 HETATM 14 C C4' DUP . . . C 3 -8.179 57.74 32.742 1 15.53 ? C4' DUP 777 A 1 HETATM 15 C C5' DUP . . . C 3 -9.318 58.766 32.519 1 18.22 ? C5' DUP 777 A 1 HETATM 16 O O5' DUP . . . C 3 -8.721 60.01 32.087 1 15.69 ? O5' DUP 777 A 1 HETATM 17 P PA DUP . . . C 3 -9.667 61.212 31.579 1 15.17 ? PA DUP 777 A 1 HETATM 18 O O1A DUP . . . C 3 -10.656 61.616 32.604 1 15.03 ? O1A DUP 777 A 1 HETATM 19 O O2A DUP . . . C 3 -8.726 62.28 31.047 1 15.84 ? O2A DUP 777 A 1 HETATM 20 N N3A DUP . . . C 3 -10.427 60.54 30.293 1 14.45 ? N3A DUP 777 A 1 HETATM 21 P PB DUP . . . C 3 -12.078 60.534 29.971 1 17.63 ? PB DUP 777 A 1 HETATM 22 O O1B DUP . . . C 3 -12.794 61.674 30.649 1 17.02 ? O1B DUP 777 A 1 HETATM 23 O O2B DUP . . . C 3 -12.223 60.497 28.483 1 21.55 ? O2B DUP 777 A 1 HETATM 24 O O3B DUP . . . C 3 -12.642 59.128 30.543 1 23.55 ? O3B DUP 777 A 1 HETATM 25 P PG DUP . . . C 3 -13.575 59.015 31.849 1 26.77 ? PG DUP 777 A 1 HETATM 26 O O2G DUP . . . C 3 -13.172 59.961 32.971 1 22.39 ? O2G DUP 777 A 1 HETATM 27 O O1G DUP . . . C 3 -14.933 59.458 31.413 1 35.93 ? O1G DUP 777 A 1 HETATM 28 O O3G DUP . . . C 3 -13.52 57.593 32.295 1 32.35 ? O3G DUP 777 A 1 # _model_server_stats.io_time_ms 6 _model_server_stats.parse_time_ms 6 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 234 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 28 #