data_1L5K # _model_server_result.job_id L4KJSaZtn8npZyyLOTmPZA _model_server_result.datetime_utc '2024-11-13 10:25:58' _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 1l5k # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"B","auth_seq_id":990}' # _entry.id 1L5K # _exptl.entry_id 1L5K _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 330.23 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "1-ALPHA-D-RIBOFURANOSYL-BENZIMIAZOLE-5'-PHOSPHATE" _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 90 _cell.entry_id 1L5K _cell.length_a 71.69 _cell.length_b 89.93 _cell.length_c 47.72 _cell.Z_PDB 4 _cell.pdbx_unique_axis ? # _symmetry.entry_id 1L5K _symmetry.cell_setting orthorhombic _symmetry.Int_Tables_number 18 _symmetry.space_group_name_Hall . _symmetry.space_group_name_H-M 'P 21 21 2' # _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_665 -x+1,-y+1,z -1 0 0 0 -1 0 0 0 1 71.69 89.93 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 # _struct_conn.conn_type_id disulf _struct_conn.details ? _struct_conn.id disulf1 _struct_conn.ptnr1_label_asym_id A _struct_conn.ptnr1_label_atom_id SG _struct_conn.ptnr1_label_comp_id CYS _struct_conn.ptnr1_label_seq_id 160 _struct_conn.ptnr1_auth_asym_id A _struct_conn.ptnr1_auth_comp_id CYS _struct_conn.ptnr1_auth_seq_id 160 _struct_conn.ptnr1_symmetry 1_555 _struct_conn.ptnr2_label_asym_id A _struct_conn.ptnr2_label_atom_id SG _struct_conn.ptnr2_label_comp_id CYS _struct_conn.ptnr2_label_seq_id 256 _struct_conn.ptnr2_auth_asym_id A _struct_conn.ptnr2_auth_comp_id CYS _struct_conn.ptnr2_auth_seq_id 256 _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 2.027 _struct_conn.pdbx_value_order ? # _chem_comp.formula 'C12 H15 N2 O7 P' _chem_comp.formula_weight 330.23 _chem_comp.id 1RB _chem_comp.mon_nstd_flag . _chem_comp.name "1-ALPHA-D-RIBOFURANOSYL-BENZIMIAZOLE-5'-PHOSPHATE" _chem_comp.type non-polymer _chem_comp.pdbx_synonyms "ALPHA-RIBAZOLE-5'-PHOSPHATE DERIVATIVE" # 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 N3 C2 1RB doub 1 n y N3 C3A 1RB sing 2 n y N1 C2 1RB sing 3 n y N1 C7A 1RB sing 4 n y N1 C1' 1RB sing 5 n n C2 H2 1RB sing 6 n n C7A C3A 1RB doub 7 n y C7A C7 1RB sing 8 n y C3A C4 1RB sing 9 n y C4 C5 1RB doub 10 n y C4 H4 1RB sing 11 n n C5 C6 1RB sing 12 n y C5 H5 1RB sing 13 n n C6 C7 1RB doub 14 n y C6 H6 1RB sing 15 n n C7 H7 1RB sing 16 n n P O1P 1RB doub 17 n n P O2P 1RB sing 18 n n P O3P 1RB sing 19 n n P O5' 1RB sing 20 n n O2P HOP2 1RB sing 21 n n O3P HOP3 1RB sing 22 n n O5' C5' 1RB sing 23 n n C5' C4' 1RB sing 24 n n C5' "H5'1" 1RB sing 25 n n C5' "H5'2" 1RB sing 26 n n C4' O4' 1RB sing 27 n n C4' C3' 1RB sing 28 n n C4' H4' 1RB sing 29 n n O4' C1' 1RB sing 30 n n C3' O3' 1RB sing 31 n n C3' C2' 1RB sing 32 n n C3' H3' 1RB sing 33 n n O3' HO23 1RB sing 34 n n C2' O2' 1RB sing 35 n n C2' C1' 1RB sing 36 n n C2' H2' 1RB sing 37 n n O2' HO22 1RB sing 38 n n C1' H1' 1RB sing 39 n n # _atom_sites.entry_id 1L5K _atom_sites.fract_transf_matrix[1][1] 0.013949 _atom_sites.fract_transf_matrix[1][2] 0 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.01112 _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] 0.020956 _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 1RB A 1 990 990 1RB 1RB . C 3 NIO A 1 991 991 NIO NIO . D 4 HOH A 1 1001 1001 HOH HOH . D 4 HOH A 2 1002 1002 HOH HOH . D 4 HOH A 3 1003 1003 HOH HOH . D 4 HOH A 4 1004 1004 HOH HOH . D 4 HOH A 5 1005 1005 HOH HOH . D 4 HOH A 6 1006 1006 HOH HOH . D 4 HOH A 7 1007 1007 HOH HOH . D 4 HOH A 8 1008 1008 HOH HOH . D 4 HOH A 9 1009 1009 HOH HOH . D 4 HOH A 10 1010 1010 HOH HOH . D 4 HOH A 11 1011 1011 HOH HOH . D 4 HOH A 12 1012 1012 HOH HOH . D 4 HOH A 13 1013 1013 HOH HOH . D 4 HOH A 14 1014 1014 HOH HOH . D 4 HOH A 15 1015 1015 HOH HOH . D 4 HOH A 16 1016 1016 HOH HOH . D 4 HOH A 17 1017 1017 HOH HOH . D 4 HOH A 18 1018 1018 HOH HOH . D 4 HOH A 19 1019 1019 HOH HOH . D 4 HOH A 20 1020 1020 HOH HOH . D 4 HOH A 21 1021 1021 HOH HOH . D 4 HOH A 22 1022 1022 HOH HOH . D 4 HOH A 23 1023 1023 HOH HOH . D 4 HOH A 24 1024 1024 HOH HOH . D 4 HOH A 25 1025 1025 HOH HOH . D 4 HOH A 26 1026 1026 HOH HOH . D 4 HOH A 27 1027 1027 HOH HOH . D 4 HOH A 28 1028 1028 HOH HOH . D 4 HOH A 29 1029 1029 HOH HOH . D 4 HOH A 30 1030 1030 HOH HOH . D 4 HOH A 31 1031 1031 HOH HOH . D 4 HOH A 32 1032 1032 HOH HOH . D 4 HOH A 33 1033 1033 HOH HOH . D 4 HOH A 34 1034 1034 HOH HOH . D 4 HOH A 35 1035 1035 HOH HOH . D 4 HOH A 36 1036 1036 HOH HOH . D 4 HOH A 37 1037 1037 HOH HOH . D 4 HOH A 38 1038 1038 HOH HOH . D 4 HOH A 39 1039 1039 HOH HOH . D 4 HOH A 40 1040 1040 HOH HOH . D 4 HOH A 41 1041 1041 HOH HOH . D 4 HOH A 42 1042 1042 HOH HOH . D 4 HOH A 43 1043 1043 HOH HOH . D 4 HOH A 44 1044 1044 HOH HOH . D 4 HOH A 45 1045 1045 HOH HOH . D 4 HOH A 46 1046 1046 HOH HOH . D 4 HOH A 47 1047 1047 HOH HOH . D 4 HOH A 48 1048 1048 HOH HOH . D 4 HOH A 49 1050 1050 HOH HOH . D 4 HOH A 50 1051 1051 HOH HOH . D 4 HOH A 51 1052 1052 HOH HOH . D 4 HOH A 52 1053 1053 HOH HOH . D 4 HOH A 53 1054 1054 HOH HOH . D 4 HOH A 54 1056 1056 HOH HOH . D 4 HOH A 55 1057 1057 HOH HOH . D 4 HOH A 56 1058 1058 HOH HOH . D 4 HOH A 57 1059 1059 HOH HOH . D 4 HOH A 58 1060 1060 HOH HOH . D 4 HOH A 59 1061 1061 HOH HOH . D 4 HOH A 60 1062 1062 HOH HOH . D 4 HOH A 61 1063 1063 HOH HOH . D 4 HOH A 62 1064 1064 HOH HOH . D 4 HOH A 63 1065 1065 HOH HOH . D 4 HOH A 64 1066 1066 HOH HOH . D 4 HOH A 65 1067 1067 HOH HOH . D 4 HOH A 66 1068 1068 HOH HOH . D 4 HOH A 67 1069 1069 HOH HOH . D 4 HOH A 68 1070 1070 HOH HOH . D 4 HOH A 69 1071 1071 HOH HOH . D 4 HOH A 70 1072 1072 HOH HOH . D 4 HOH A 71 1073 1073 HOH HOH . D 4 HOH A 72 1074 1074 HOH HOH . D 4 HOH A 73 1075 1075 HOH HOH . D 4 HOH A 74 1076 1076 HOH HOH . D 4 HOH A 75 1077 1077 HOH HOH . D 4 HOH A 76 1079 1079 HOH HOH . D 4 HOH A 77 1080 1080 HOH HOH . D 4 HOH A 78 1082 1082 HOH HOH . D 4 HOH A 79 1083 1083 HOH HOH . D 4 HOH A 80 1085 1085 HOH HOH . D 4 HOH A 81 1087 1087 HOH HOH . D 4 HOH A 82 1088 1088 HOH HOH . D 4 HOH A 83 1089 1089 HOH HOH . D 4 HOH A 84 1090 1090 HOH HOH . D 4 HOH A 85 1092 1092 HOH HOH . D 4 HOH A 86 1093 1093 HOH HOH . D 4 HOH A 87 1094 1094 HOH HOH . D 4 HOH A 88 1095 1095 HOH HOH . D 4 HOH A 89 1096 1096 HOH HOH . D 4 HOH A 90 1098 1098 HOH HOH . D 4 HOH A 91 1099 1099 HOH HOH . D 4 HOH A 92 1100 1100 HOH HOH . D 4 HOH A 93 1101 1101 HOH HOH . D 4 HOH A 94 1102 1102 HOH HOH . D 4 HOH A 95 1103 1103 HOH HOH . D 4 HOH A 96 1104 1104 HOH HOH . D 4 HOH A 97 1105 1105 HOH HOH . D 4 HOH A 98 1106 1106 HOH HOH . D 4 HOH A 99 1107 1107 HOH HOH . D 4 HOH A 100 1108 1108 HOH HOH . D 4 HOH A 101 1109 1109 HOH HOH . D 4 HOH A 102 1111 1111 HOH HOH . D 4 HOH A 103 1112 1112 HOH HOH . D 4 HOH A 104 1113 1113 HOH HOH . D 4 HOH A 105 1114 1114 HOH HOH . D 4 HOH A 106 1115 1115 HOH HOH . D 4 HOH A 107 1116 1116 HOH HOH . D 4 HOH A 108 1118 1118 HOH HOH . D 4 HOH A 109 1119 1119 HOH HOH . D 4 HOH A 110 1122 1122 HOH HOH . D 4 HOH A 111 1126 1126 HOH HOH . D 4 HOH A 112 1150 1150 HOH HOH . D 4 HOH A 113 1151 1151 HOH HOH . D 4 HOH A 114 1152 1152 HOH HOH . D 4 HOH A 115 1153 1153 HOH HOH . D 4 HOH A 116 1154 1154 HOH HOH . D 4 HOH A 117 1155 1155 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 N3 1RB . . . B 2 56.347 41.611 14.094 1 9.53 ? N3 1RB 990 A 1 HETATM 2 N N1 1RB . . . B 2 56.621 40.906 11.923 1 7.74 ? N1 1RB 990 A 1 HETATM 3 C C2 1RB . . . B 2 55.848 40.934 13.053 1 9.08 ? C2 1RB 990 A 1 HETATM 4 C C7A 1RB . . . B 2 57.762 41.669 12.327 1 9.07 ? C7A 1RB 990 A 1 HETATM 5 C C3A 1RB . . . B 2 57.564 42.105 13.693 1 10.27 ? C3A 1RB 990 A 1 HETATM 6 C C4 1RB . . . B 2 58.538 42.896 14.369 1 10.82 ? C4 1RB 990 A 1 HETATM 7 C C5 1RB . . . B 2 59.714 43.259 13.687 1 11.85 ? C5 1RB 990 A 1 HETATM 8 C C6 1RB . . . B 2 59.933 42.839 12.324 1 8.34 ? C6 1RB 990 A 1 HETATM 9 C C7 1RB . . . B 2 58.968 42.052 11.643 1 10.77 ? C7 1RB 990 A 1 HETATM 10 P P 1RB . . . B 2 59.27 39.315 6.026 1 11.1 ? P 1RB 990 A 1 HETATM 11 O O1P 1RB . . . B 2 59.049 38.066 5.233 1 8.98 ? O1P 1RB 990 A 1 HETATM 12 O O2P 1RB . . . B 2 59.548 40.466 5.115 1 7.99 ? O2P 1RB 990 A 1 HETATM 13 O O3P 1RB . . . B 2 60.434 39.125 6.952 1 9.94 ? O3P 1RB 990 A 1 HETATM 14 O O5' 1RB . . . B 2 57.956 39.641 6.898 1 10.83 ? O5' 1RB 990 A 1 HETATM 15 C C5' 1RB . . . B 2 57.469 38.691 7.845 1 11.59 ? C5' 1RB 990 A 1 HETATM 16 C C4' 1RB . . . B 2 57.951 39.095 9.241 1 9.46 ? C4' 1RB 990 A 1 HETATM 17 O O4' 1RB . . . B 2 57.405 40.397 9.653 1 10.46 ? O4' 1RB 990 A 1 HETATM 18 C C3' 1RB . . . B 2 57.525 38.167 10.365 1 9.55 ? C3' 1RB 990 A 1 HETATM 19 O O3' 1RB . . . B 2 58.402 38.248 11.51 1 11.33 ? O3' 1RB 990 A 1 HETATM 20 C C2' 1RB . . . B 2 56.152 38.717 10.655 1 9.12 ? C2' 1RB 990 A 1 HETATM 21 O O2' 1RB . . . B 2 55.702 38.225 11.919 1 9.2 ? O2' 1RB 990 A 1 HETATM 22 C C1' 1RB . . . B 2 56.334 40.224 10.584 1 9.86 ? C1' 1RB 990 A 1 # _model_server_stats.io_time_ms 58 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 4 _model_server_stats.query_time_ms 282 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 22 #