data_1INI # _model_server_result.job_id NcegllBotAzchT9vEc-Q8w _model_server_result.datetime_utc '2024-11-26 13:17:47' _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 1ini # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":1001}' # _entry.id 1INI # _exptl.entry_id 1INI _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 521.308 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL _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 92.64 _cell.angle_gamma 90 _cell.entry_id 1INI _cell.length_a 129.99 _cell.length_b 46.764 _cell.length_c 38.387 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1INI _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,PQS _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_656 -x+1,y,-z+1 -1 0 0 0 1 0 0 0 -1 128.22188 0 38.346258 # _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 # _struct_conn.conn_type_id metalc _struct_conn.details ? _struct_conn.id metalc1 _struct_conn.ptnr1_label_asym_id C _struct_conn.ptnr1_label_atom_id O2A _struct_conn.ptnr1_label_comp_id CDM _struct_conn.ptnr1_label_seq_id . _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CDM _struct_conn.ptnr1_auth_seq_id 1001 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id B _struct_conn.ptnr2_label_atom_id MG _struct_conn.ptnr2_label_comp_id MG _struct_conn.ptnr2_label_seq_id . _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id MG _struct_conn.ptnr2_auth_seq_id 1002 _struct_conn.ptnr2_symmetry 1_555 _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 2.666 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C14 H25 N3 O14 P2' _chem_comp.formula_weight 521.308 _chem_comp.id CDM _chem_comp.mon_nstd_flag . _chem_comp.name 4-DIPHOSPHOCYTIDYL-2-C-METHYL-D-ERYTHRITOL _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 CDM sing 70 n n N1 C6 CDM sing 71 n n N1 C1' CDM sing 72 n n C2 N3 CDM sing 73 n n C2 O2 CDM doub 74 n n N3 C4 CDM doub 75 n n C4 C5 CDM sing 76 n n C4 N4 CDM sing 77 n n C5 C6 CDM doub 78 n n C5 H5 CDM sing 79 n n C6 H6 CDM sing 80 n n N4 H41 CDM sing 81 n n N4 H42 CDM sing 82 n n C1' C2' CDM sing 83 n n C1' O4' CDM sing 84 n n C1' H1' CDM sing 85 n n C2' O2' CDM sing 86 n n C2' C3' CDM sing 87 n n C2' H2' CDM sing 88 n n O2' "HO'2" CDM sing 89 n n C3' C4' CDM sing 90 n n C3' O3' CDM sing 91 n n C3' H3' CDM sing 92 n n C4' O4' CDM sing 93 n n C4' C5' CDM sing 94 n n C4' H4' CDM sing 95 n n O3' H3T CDM sing 96 n n C5' O5' CDM sing 97 n n C5' "H5'1" CDM sing 98 n n C5' "H5'2" CDM sing 99 n n O5' PA CDM sing 100 n n PA O1A CDM doub 101 n n PA O2A CDM sing 102 n n PA O3A CDM sing 103 n n O2A HO2A CDM sing 104 n n O3A PB CDM sing 105 n n PB O1B CDM sing 106 n n PB O2B CDM doub 107 n n PB O3B CDM sing 108 n n O1B HO1B CDM sing 109 n n O3B C1M CDM sing 110 n n C1M C2M CDM sing 111 n n C1M H1M1 CDM sing 112 n n C1M H1M2 CDM sing 113 n n C2M O2M CDM sing 114 n n C2M C3M CDM sing 115 n n C2M H2M1 CDM sing 116 n n O2M H2M2 CDM sing 117 n n C3M C4M CDM sing 118 n n C3M C5M CDM sing 119 n n C3M O3M CDM sing 120 n n C4M O4M CDM sing 121 n n C4M H4M1 CDM sing 122 n n C4M H4M2 CDM sing 123 n n C5M H5M1 CDM sing 124 n n C5M H5M2 CDM sing 125 n n C5M H5M3 CDM sing 126 n n O3M H3M CDM sing 127 n n O4M H4M CDM sing 128 n n # _atom_sites.entry_id 1INI _atom_sites.fract_transf_matrix[1][1] 0.007693 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0.000354 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.021384 _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] 0.026078 _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 1002 1 MG MG2 . C 3 CDM A 1 1001 1 CDM PRD . D 4 HOH A 1 1003 1 HOH WAT . D 4 HOH A 2 1004 2 HOH WAT . D 4 HOH A 3 1005 3 HOH WAT . D 4 HOH A 4 1006 4 HOH WAT . D 4 HOH A 5 1007 5 HOH WAT . D 4 HOH A 6 1008 6 HOH WAT . D 4 HOH A 7 1009 7 HOH WAT . D 4 HOH A 8 1010 8 HOH WAT . D 4 HOH A 9 1011 9 HOH WAT . D 4 HOH A 10 1012 10 HOH WAT . D 4 HOH A 11 1013 11 HOH WAT . D 4 HOH A 12 1014 12 HOH WAT . D 4 HOH A 13 1015 13 HOH WAT . D 4 HOH A 14 1016 14 HOH WAT . D 4 HOH A 15 1017 15 HOH WAT . D 4 HOH A 16 1018 16 HOH WAT . D 4 HOH A 17 1019 17 HOH WAT . D 4 HOH A 18 1020 18 HOH WAT . D 4 HOH A 19 1021 19 HOH WAT . D 4 HOH A 20 1022 20 HOH WAT . D 4 HOH A 21 1023 21 HOH WAT . D 4 HOH A 22 1024 22 HOH WAT . D 4 HOH A 23 1025 23 HOH WAT . D 4 HOH A 24 1026 24 HOH WAT . D 4 HOH A 25 1027 25 HOH WAT . D 4 HOH A 26 1028 26 HOH WAT . D 4 HOH A 27 1029 27 HOH WAT . D 4 HOH A 28 1030 28 HOH WAT . D 4 HOH A 29 1031 29 HOH WAT . D 4 HOH A 30 1032 30 HOH WAT . D 4 HOH A 31 1033 31 HOH WAT . D 4 HOH A 32 1034 32 HOH WAT . D 4 HOH A 33 1035 33 HOH WAT . D 4 HOH A 34 1036 34 HOH WAT . D 4 HOH A 35 1037 35 HOH WAT . D 4 HOH A 36 1038 36 HOH WAT . D 4 HOH A 37 1039 37 HOH WAT . D 4 HOH A 38 1040 38 HOH WAT . D 4 HOH A 39 1041 39 HOH WAT . D 4 HOH A 40 1042 40 HOH WAT . D 4 HOH A 41 1043 41 HOH WAT . D 4 HOH A 42 1044 42 HOH WAT . D 4 HOH A 43 1045 43 HOH WAT . D 4 HOH A 44 1046 44 HOH WAT . D 4 HOH A 45 1047 45 HOH WAT . D 4 HOH A 46 1048 46 HOH WAT . D 4 HOH A 47 1049 47 HOH WAT . D 4 HOH A 48 1050 48 HOH WAT . D 4 HOH A 49 1051 49 HOH WAT . D 4 HOH A 50 1052 50 HOH WAT . D 4 HOH A 51 1053 51 HOH WAT . D 4 HOH A 52 1054 52 HOH WAT . D 4 HOH A 53 1055 53 HOH WAT . D 4 HOH A 54 1056 54 HOH WAT . D 4 HOH A 55 1057 55 HOH WAT . D 4 HOH A 56 1058 56 HOH WAT . D 4 HOH A 57 1059 57 HOH WAT . D 4 HOH A 58 1060 58 HOH WAT . D 4 HOH A 59 1061 59 HOH WAT . D 4 HOH A 60 1062 60 HOH WAT . D 4 HOH A 61 1063 61 HOH WAT . D 4 HOH A 62 1064 62 HOH WAT . D 4 HOH A 63 1065 63 HOH WAT . D 4 HOH A 64 1066 64 HOH WAT . D 4 HOH A 65 1067 65 HOH WAT . D 4 HOH A 66 1068 66 HOH WAT . D 4 HOH A 67 1069 67 HOH WAT . D 4 HOH A 68 1070 68 HOH WAT . D 4 HOH A 69 1071 69 HOH WAT . D 4 HOH A 70 1072 70 HOH WAT . D 4 HOH A 71 1073 71 HOH WAT . D 4 HOH A 72 1074 72 HOH WAT . D 4 HOH A 73 1075 73 HOH WAT . D 4 HOH A 74 1076 74 HOH WAT . D 4 HOH A 75 1077 75 HOH WAT . D 4 HOH A 76 1078 76 HOH WAT . D 4 HOH A 77 1079 77 HOH WAT . D 4 HOH A 78 1080 78 HOH WAT . D 4 HOH A 79 1081 79 HOH WAT . D 4 HOH A 80 1082 80 HOH WAT . D 4 HOH A 81 1083 81 HOH WAT . D 4 HOH A 82 1084 82 HOH WAT . D 4 HOH A 83 1085 83 HOH WAT . D 4 HOH A 84 1086 84 HOH WAT . D 4 HOH A 85 1087 85 HOH WAT . D 4 HOH A 86 1088 86 HOH WAT . D 4 HOH A 87 1089 87 HOH WAT . D 4 HOH A 88 1090 88 HOH WAT . D 4 HOH A 89 1091 89 HOH WAT . D 4 HOH A 90 1092 90 HOH WAT . D 4 HOH A 91 1093 91 HOH WAT . D 4 HOH A 92 1094 92 HOH WAT . D 4 HOH A 93 1095 93 HOH WAT . D 4 HOH A 94 1096 94 HOH WAT . D 4 HOH A 95 1097 95 HOH WAT . D 4 HOH A 96 1098 96 HOH WAT . D 4 HOH A 97 1099 97 HOH WAT . D 4 HOH A 98 1100 98 HOH WAT . D 4 HOH A 99 1101 100 HOH WAT . D 4 HOH A 100 1102 102 HOH WAT . D 4 HOH A 101 1103 103 HOH WAT . D 4 HOH A 102 1104 104 HOH WAT . D 4 HOH A 103 1105 111 HOH WAT . # 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 CDM . . . C 3 48.972 -15.32 32.129 1 29.02 ? N1 CDM 1001 A 1 HETATM 2 C C2 CDM . . . C 3 47.711 -15.455 32.8 1 29.67 ? C2 CDM 1001 A 1 HETATM 3 N N3 CDM . . . C 3 47.604 -16.211 33.929 1 32.81 ? N3 CDM 1001 A 1 HETATM 4 C C4 CDM . . . C 3 48.759 -16.883 34.469 1 38.96 ? C4 CDM 1001 A 1 HETATM 5 C C5 CDM . . . C 3 50.037 -16.794 33.854 1 37.47 ? C5 CDM 1001 A 1 HETATM 6 C C6 CDM . . . C 3 50.086 -16.008 32.703 1 36.83 ? C6 CDM 1001 A 1 HETATM 7 O O2 CDM . . . C 3 46.649 -14.916 32.422 1 26.63 ? O2 CDM 1001 A 1 HETATM 8 N N4 CDM . . . C 3 48.591 -17.609 35.589 1 41.17 ? N4 CDM 1001 A 1 HETATM 9 C C1' CDM . . . C 3 49.134 -14.495 30.891 1 25.2 ? C1' CDM 1001 A 1 HETATM 10 C C2' CDM . . . C 3 50.055 -13.319 31.132 1 22.87 ? C2' CDM 1001 A 1 HETATM 11 O O2' CDM . . . C 3 49.351 -12.35 31.855 1 28.07 ? O2' CDM 1001 A 1 HETATM 12 C C3' CDM . . . C 3 50.529 -12.941 29.743 1 31.3 ? C3' CDM 1001 A 1 HETATM 13 C C4' CDM . . . C 3 50.336 -14.252 28.943 1 26.22 ? C4' CDM 1001 A 1 HETATM 14 O O4' CDM . . . C 3 49.735 -15.21 29.845 1 26.22 ? O4' CDM 1001 A 1 HETATM 15 O O3' CDM . . . C 3 49.677 -11.98 29.08 1 28.78 ? O3' CDM 1001 A 1 HETATM 16 C C5' CDM . . . C 3 51.739 -14.679 28.527 1 25.12 ? C5' CDM 1001 A 1 HETATM 17 O O5' CDM . . . C 3 52.433 -15.082 29.674 1 34.01 ? O5' CDM 1001 A 1 HETATM 18 P PA CDM . . . C 3 54.056 -15.077 29.828 1 34.69 ? PA CDM 1001 A 1 HETATM 19 O O1A CDM . . . C 3 54.488 -13.616 29.398 1 37.03 ? O1A CDM 1001 A 1 HETATM 20 O O2A CDM . . . C 3 54.346 -15.458 31.47 1 41.29 ? O2A CDM 1001 A 1 HETATM 21 O O3A CDM . . . C 3 54.497 -16.134 28.879 1 36.65 ? O3A CDM 1001 A 1 HETATM 22 P PB CDM . . . C 3 54.585 -17.612 28.672 1 32.41 ? PB CDM 1001 A 1 HETATM 23 O O1B CDM . . . C 3 53.337 -18.265 29.179 1 38.87 ? O1B CDM 1001 A 1 HETATM 24 O O2B CDM . . . C 3 55.839 -18.087 29.434 1 31.39 ? O2B CDM 1001 A 1 HETATM 25 O O3B CDM . . . C 3 54.687 -18.2 27.3 1 39.88 ? O3B CDM 1001 A 1 HETATM 26 C C1M CDM . . . C 3 53.636 -17.827 26.427 1 29.1 ? C1M CDM 1001 A 1 HETATM 27 C C2M CDM . . . C 3 54.008 -18.44 25.091 1 25.19 ? C2M CDM 1001 A 1 HETATM 28 O O2M CDM . . . C 3 53.969 -19.941 25.302 1 21.21 ? O2M CDM 1001 A 1 HETATM 29 C C3M CDM . . . C 3 53.045 -18.056 23.911 1 27.61 ? C3M CDM 1001 A 1 HETATM 30 C C4M CDM . . . C 3 53.514 -18.842 22.709 1 27.06 ? C4M CDM 1001 A 1 HETATM 31 C C5M CDM . . . C 3 51.561 -18.347 24.271 1 22.78 ? C5M CDM 1001 A 1 HETATM 32 O O3M CDM . . . C 3 53.182 -16.597 23.532 1 25.74 ? O3M CDM 1001 A 1 HETATM 33 O O4M CDM . . . C 3 54.967 -18.442 22.335 1 25.83 ? O4M CDM 1001 A 1 # _model_server_stats.io_time_ms 51 _model_server_stats.parse_time_ms 5 _model_server_stats.create_model_time_ms 2 _model_server_stats.query_time_ms 250 _model_server_stats.encode_time_ms 5 _model_server_stats.element_count 33 #