data_2OD7 # _model_server_result.job_id QPImo394ta-PomDIwvm4-Q _model_server_result.datetime_utc '2024-11-15 03:35:00' _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 2od7 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":1001}' # _entry.id 2OD7 # _exptl.entry_id 2OD7 _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 2OD7 _cell.length_a 106.759 _cell.length_b 106.759 _cell.length_c 67.689 _cell.Z_PDB 6 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2OD7 _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 dimeric 2 author_and_software_defined_assembly 1 PISA tetrameric 4 software_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 A,B,C,D,E,F 2 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' 4_556 y,x,-z+1 -0.5 0.866025 0 0.866025 0.5 0 0 0 -1 0 0 67.689 # _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 ? ? ? ? ? ? ? ? ? ? ? ? 1.398 ? covale ? covale2 B O ALY 5 B ALY 16 1_555 B N ARG 6 B ARG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.949 ? covale ? covale3 B C ALY 5 B ALY 16 1_555 B N ARG 6 B ARG 17 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.146 ? metalc ? metalc1 A SG CYS 157 A CYS 143 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.381 ? metalc ? metalc2 A SG CYS 160 A CYS 146 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.313 ? metalc ? metalc3 A SG CYS 184 A CYS 170 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.352 ? metalc ? metalc4 A SG CYS 187 A CYS 173 1_555 C ZN ZN . A ZN 701 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.441 ? # _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 2OD7 _atom_sites.fract_transf_matrix[1][1] 0.009367 _atom_sites.fract_transf_matrix[1][2] 0.005408 _atom_sites.fract_transf_matrix[1][3] 0 _atom_sites.fract_transf_matrix[2][1] 0 _atom_sites.fract_transf_matrix[2][2] 0.010816 _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] 0.014773 _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 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 7 HOH HOH . E 5 HOH A 8 1009 8 HOH HOH . E 5 HOH A 9 1010 9 HOH HOH . E 5 HOH A 10 1011 10 HOH HOH . E 5 HOH A 11 1012 11 HOH HOH . E 5 HOH A 12 1013 12 HOH HOH . E 5 HOH A 13 1014 13 HOH HOH . E 5 HOH A 14 1015 14 HOH HOH . E 5 HOH A 15 1016 15 HOH HOH . E 5 HOH A 16 1017 16 HOH HOH . E 5 HOH A 17 1018 17 HOH HOH . E 5 HOH A 18 1019 18 HOH HOH . E 5 HOH A 19 1020 19 HOH HOH . E 5 HOH A 20 1021 20 HOH HOH . E 5 HOH A 21 1022 21 HOH HOH . E 5 HOH A 22 1023 22 HOH HOH . E 5 HOH A 23 1024 23 HOH HOH . E 5 HOH A 24 1025 24 HOH HOH . E 5 HOH A 25 1026 25 HOH HOH . E 5 HOH A 26 1027 26 HOH HOH . E 5 HOH A 27 1028 27 HOH HOH . E 5 HOH A 28 1029 28 HOH HOH . E 5 HOH A 29 1030 29 HOH HOH . E 5 HOH A 30 1031 30 HOH HOH . E 5 HOH A 31 1032 31 HOH HOH . E 5 HOH A 32 1033 32 HOH HOH . E 5 HOH A 33 1034 33 HOH HOH . E 5 HOH A 34 1035 34 HOH HOH . E 5 HOH A 35 1036 35 HOH HOH . E 5 HOH A 36 1037 36 HOH HOH . E 5 HOH A 37 1038 37 HOH HOH . E 5 HOH A 38 1039 38 HOH HOH . E 5 HOH A 39 1040 39 HOH HOH . E 5 HOH A 40 1041 40 HOH HOH . E 5 HOH A 41 1042 41 HOH HOH . E 5 HOH A 42 1043 42 HOH HOH . E 5 HOH A 43 1044 43 HOH HOH . E 5 HOH A 44 1045 44 HOH HOH . E 5 HOH A 45 1046 45 HOH HOH . E 5 HOH A 46 1047 46 HOH HOH . E 5 HOH A 47 1048 47 HOH HOH . E 5 HOH A 48 1049 48 HOH HOH . E 5 HOH A 49 1050 50 HOH HOH . E 5 HOH A 50 1051 51 HOH HOH . E 5 HOH A 51 1052 53 HOH HOH . E 5 HOH A 52 1053 54 HOH HOH . E 5 HOH A 53 1054 55 HOH HOH . E 5 HOH A 54 1055 56 HOH HOH . E 5 HOH A 55 1056 57 HOH HOH . E 5 HOH A 56 1057 58 HOH HOH . E 5 HOH A 57 1058 59 HOH HOH . E 5 HOH A 58 1059 60 HOH HOH . E 5 HOH A 59 1060 61 HOH HOH . E 5 HOH A 60 1061 62 HOH HOH . E 5 HOH A 61 1062 63 HOH HOH . E 5 HOH A 62 1063 64 HOH HOH . E 5 HOH A 63 1064 65 HOH HOH . E 5 HOH A 64 1065 66 HOH HOH . E 5 HOH A 65 1066 67 HOH HOH . E 5 HOH A 66 1067 68 HOH HOH . E 5 HOH A 67 1068 69 HOH HOH . E 5 HOH A 68 1069 70 HOH HOH . E 5 HOH A 69 1070 71 HOH HOH . E 5 HOH A 70 1071 72 HOH HOH . E 5 HOH A 71 1072 73 HOH HOH . E 5 HOH A 72 1073 74 HOH HOH . E 5 HOH A 73 1074 75 HOH HOH . E 5 HOH A 74 1075 76 HOH HOH . E 5 HOH A 75 1076 77 HOH HOH . E 5 HOH A 76 1077 78 HOH HOH . E 5 HOH A 77 1078 79 HOH HOH . E 5 HOH A 78 1079 80 HOH HOH . E 5 HOH A 79 1080 81 HOH HOH . E 5 HOH A 80 1081 82 HOH HOH . E 5 HOH A 81 1082 83 HOH HOH . E 5 HOH A 82 1083 84 HOH HOH . E 5 HOH A 83 1084 85 HOH HOH . E 5 HOH A 84 1085 86 HOH HOH . E 5 HOH A 85 1086 87 HOH HOH . E 5 HOH A 86 1087 88 HOH HOH . E 5 HOH A 87 1088 89 HOH HOH . E 5 HOH A 88 1089 90 HOH HOH . E 5 HOH A 89 1090 91 HOH HOH . E 5 HOH A 90 1091 92 HOH HOH . E 5 HOH A 91 1092 93 HOH HOH . E 5 HOH A 92 1093 94 HOH HOH . E 5 HOH A 93 1094 95 HOH HOH . E 5 HOH A 94 1095 96 HOH HOH . E 5 HOH A 95 1096 97 HOH HOH . E 5 HOH A 96 1097 98 HOH HOH . E 5 HOH A 97 1098 99 HOH HOH . E 5 HOH A 98 1099 100 HOH HOH . E 5 HOH A 99 1100 101 HOH HOH . E 5 HOH A 100 1101 102 HOH HOH . E 5 HOH A 101 1102 103 HOH HOH . E 5 HOH A 102 1103 104 HOH HOH . E 5 HOH A 103 1104 105 HOH HOH . E 5 HOH A 104 1105 106 HOH HOH . E 5 HOH A 105 1106 107 HOH HOH . E 5 HOH A 106 1107 108 HOH HOH . E 5 HOH A 107 1108 109 HOH HOH . E 5 HOH A 108 1109 110 HOH HOH . E 5 HOH A 109 1110 111 HOH HOH . E 5 HOH A 110 1111 112 HOH HOH . E 5 HOH A 111 1112 113 HOH HOH . E 5 HOH A 112 1113 114 HOH HOH . E 5 HOH A 113 1114 115 HOH HOH . E 5 HOH A 114 1115 116 HOH HOH . E 5 HOH A 115 1116 117 HOH HOH . E 5 HOH A 116 1117 118 HOH HOH . E 5 HOH A 117 1118 119 HOH HOH . E 5 HOH A 118 1119 120 HOH HOH . E 5 HOH A 119 1120 121 HOH HOH . E 5 HOH A 120 1121 122 HOH HOH . E 5 HOH A 121 1122 123 HOH HOH . E 5 HOH A 122 1123 124 HOH HOH . E 5 HOH A 123 1124 125 HOH HOH . E 5 HOH A 124 1125 126 HOH HOH . E 5 HOH A 125 1126 127 HOH HOH . E 5 HOH A 126 1127 128 HOH HOH . E 5 HOH A 127 1128 129 HOH HOH . E 5 HOH A 128 1129 130 HOH HOH . E 5 HOH A 129 1130 131 HOH HOH . E 5 HOH A 130 1131 132 HOH HOH . E 5 HOH A 131 1132 133 HOH HOH . F 5 HOH B 1 49 49 HOH HOH . F 5 HOH B 2 52 52 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 39.986 59.435 23.849 1 39.96 ? N1 A1R 1001 A 1 HETATM 2 C C2 A1R . . . D 4 41.075 60.308 24.105 1 39.88 ? C2 A1R 1001 A 1 HETATM 3 N N3 A1R . . . D 4 41.421 60.754 25.452 1 37.26 ? N3 A1R 1001 A 1 HETATM 4 C C4 A1R . . . D 4 40.559 60.227 26.486 1 35.86 ? C4 A1R 1001 A 1 HETATM 5 C C5 A1R . . . D 4 39.456 59.361 26.349 1 36.63 ? C5 A1R 1001 A 1 HETATM 6 C C6 A1R . . . D 4 39.16 58.948 24.94 1 37.71 ? C6 A1R 1001 A 1 HETATM 7 N N6 A1R . . . D 4 38.092 58.078 24.601 1 40.9 ? N6 A1R 1001 A 1 HETATM 8 N N7 A1R . . . D 4 38.893 59.088 27.584 1 38.25 ? N7 A1R 1001 A 1 HETATM 9 C C8 A1R . . . D 4 39.633 59.765 28.469 1 37.6 ? C8 A1R 1001 A 1 HETATM 10 N N9 A1R . . . D 4 40.662 60.475 27.845 1 40.93 ? N9 A1R 1001 A 1 HETATM 11 C C1' A1R . . . D 4 41.73 61.34 28.367 1 39.01 ? C1' A1R 1001 A 1 HETATM 12 C C2' A1R . . . D 4 41.489 62.285 29.469 1 39.25 ? C2' A1R 1001 A 1 HETATM 13 O O2' A1R . . . D 4 41.264 63.633 28.973 1 42.99 ? O2' A1R 1001 A 1 HETATM 14 C C3' A1R . . . D 4 42.681 62.187 30.352 1 37.23 ? C3' A1R 1001 A 1 HETATM 15 O O3' A1R . . . D 4 43.648 63.258 30.222 1 40.59 ? O3' A1R 1001 A 1 HETATM 16 O O4' A1R . . . D 4 42.71 60.432 28.79 1 36.92 ? O4' A1R 1001 A 1 HETATM 17 C C4' A1R . . . D 4 43.344 60.862 30.015 1 38.93 ? C4' A1R 1001 A 1 HETATM 18 C C5' A1R . . . D 4 43.174 59.708 31.057 1 36.79 ? C5' A1R 1001 A 1 HETATM 19 O O5' A1R . . . D 4 43.773 60.105 32.332 1 37.64 ? O5' A1R 1001 A 1 HETATM 20 P PA A1R . . . D 4 43.794 59.187 33.573 1 38.58 ? PA A1R 1001 A 1 HETATM 21 O O1A A1R . . . D 4 42.45 58.701 33.941 1 43.47 ? O1A A1R 1001 A 1 HETATM 22 O O2A A1R . . . D 4 44.453 59.921 34.664 1 43 ? O2A A1R 1001 A 1 HETATM 23 O O3A A1R . . . D 4 44.752 58.01 33.379 1 38.42 ? O3A A1R 1001 A 1 HETATM 24 P PB A1R . . . D 4 46.166 57.737 32.996 1 37.71 ? PB A1R 1001 A 1 HETATM 25 O O1B A1R . . . D 4 46.859 58.991 32.691 1 40.5 ? O1B A1R 1001 A 1 HETATM 26 O O2B A1R . . . D 4 46.471 56.956 31.873 1 41.4 ? O2B A1R 1001 A 1 HETATM 27 O O5N A1R . . . D 4 46.577 57.356 34.413 1 39.37 ? O5N A1R 1001 A 1 HETATM 28 C C5N A1R . . . D 4 46.305 56.333 35.251 1 49.75 ? C5N A1R 1001 A 1 HETATM 29 N N4N A1R . . . D 4 45.254 55.296 36.79 1 51.51 ? N4N A1R 1001 A 1 HETATM 30 C C1N A1R . . . D 4 45.826 54.816 38.076 1 46.91 ? C1N A1R 1001 A 1 HETATM 31 O O2N A1R . . . D 4 45.655 56.299 39.43 1 50.16 ? O2N A1R 1001 A 1 HETATM 32 C C2N A1R . . . D 4 46.699 55.757 38.571 1 47.93 ? C2N A1R 1001 A 1 HETATM 33 O O3N A1R . . . D 4 46.716 58.282 38.148 1 58.24 ? O3N A1R 1001 A 1 HETATM 34 C C3N A1R . . . D 4 46.824 56.923 37.729 1 54.17 ? C3N A1R 1001 A 1 HETATM 35 C C4N A1R . . . D 4 45.891 56.638 36.568 1 52.15 ? C4N A1R 1001 A 1 # _model_server_stats.io_time_ms 20 _model_server_stats.parse_time_ms 26 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 275 _model_server_stats.encode_time_ms 7 _model_server_stats.element_count 35 #