data_2ONY # _model_server_result.job_id 6QsWlXW_0r06F7TmHDgOaQ _model_server_result.datetime_utc '2025-02-17 18:17:58' _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 2ony # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"F","auth_seq_id":3002}' # _entry.id 2ONY # _exptl.entry_id 2ONY _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 384.411 _entity.id 2 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description S-ADENOSYL-L-HOMOCYSTEINE _entity.pdbx_number_of_molecules 2 _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 2ONY _cell.length_a 93.96 _cell.length_b 93.96 _cell.length_c 188.03 _cell.Z_PDB 16 _cell.pdbx_unique_axis ? # _symmetry.entry_id 2ONY _symmetry.cell_setting ? _symmetry.Int_Tables_number 96 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 43 21 2' # loop_ _pdbx_struct_assembly.method_details _pdbx_struct_assembly.oligomeric_details _pdbx_struct_assembly.oligomeric_count _pdbx_struct_assembly.details _pdbx_struct_assembly.id PQS monomeric 1 author_and_software_defined_assembly 1 PQS monomeric 1 author_and_software_defined_assembly 2 PISA dimeric 2 software_defined_assembly 3 # loop_ _pdbx_struct_assembly_gen.asym_id_list _pdbx_struct_assembly_gen.assembly_id _pdbx_struct_assembly_gen.oper_expression A,C,D,G 1 1 B,E,F,H 2 1 A,B,C,D,E,F,G,H 3 1 # _pdbx_struct_oper_list.id 1 _pdbx_struct_oper_list.type 'identity operation' _pdbx_struct_oper_list.name 1_555 _pdbx_struct_oper_list.symmetry_operation x,y,z _pdbx_struct_oper_list.matrix[1][1] 1 _pdbx_struct_oper_list.matrix[1][2] 0 _pdbx_struct_oper_list.matrix[1][3] 0 _pdbx_struct_oper_list.matrix[2][1] 0 _pdbx_struct_oper_list.matrix[2][2] 1 _pdbx_struct_oper_list.matrix[2][3] 0 _pdbx_struct_oper_list.matrix[3][1] 0 _pdbx_struct_oper_list.matrix[3][2] 0 _pdbx_struct_oper_list.matrix[3][3] 1 _pdbx_struct_oper_list.vector[1] 0 _pdbx_struct_oper_list.vector[2] 0 _pdbx_struct_oper_list.vector[3] 0 # loop_ _struct_asym.details _struct_asym.entity_id _struct_asym.id _struct_asym.pdbx_modified _struct_asym.pdbx_blank_PDB_chainid_flag ? 2 C N N ? 2 F N 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 disulf ? disulf1 A SG CYS 48 A CYS 48 1_555 B SG CYS 139 B CYS 639 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.044 ? disulf ? disulf2 A SG CYS 139 A CYS 139 1_555 B SG CYS 48 B CYS 548 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.042 ? # _chem_comp.formula 'C14 H20 N6 O5 S' _chem_comp.formula_weight 384.411 _chem_comp.id SAH _chem_comp.mon_nstd_flag . _chem_comp.name S-ADENOSYL-L-HOMOCYSTEINE _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 N CA SAH sing 281 n n N HN1 SAH sing 282 n n N HN2 SAH sing 283 n n CA CB SAH sing 284 n n CA C SAH sing 285 n n CA HA SAH sing 286 n n CB CG SAH sing 287 n n CB HB1 SAH sing 288 n n CB HB2 SAH sing 289 n n CG SD SAH sing 290 n n CG HG1 SAH sing 291 n n CG HG2 SAH sing 292 n n SD C5' SAH sing 293 n n C O SAH doub 294 n n C OXT SAH sing 295 n n OXT HXT SAH sing 296 n n C5' C4' SAH sing 297 n n C5' "H5'1" SAH sing 298 n n C5' "H5'2" SAH sing 299 n n C4' O4' SAH sing 300 n n C4' C3' SAH sing 301 n n C4' H4' SAH sing 302 n n O4' C1' SAH sing 303 n n C3' O3' SAH sing 304 n n C3' C2' SAH sing 305 n n C3' H3' SAH sing 306 n n O3' HO3' SAH sing 307 n n C2' O2' SAH sing 308 n n C2' C1' SAH sing 309 n n C2' H2' SAH sing 310 n n O2' HO2' SAH sing 311 n n C1' N9 SAH sing 312 n n C1' H1' SAH sing 313 n n N9 C8 SAH sing 314 n y N9 C4 SAH sing 315 n y C8 N7 SAH doub 316 n y C8 H8 SAH sing 317 n n N7 C5 SAH sing 318 n y C5 C6 SAH sing 319 n y C5 C4 SAH doub 320 n y C6 N6 SAH sing 321 n n C6 N1 SAH doub 322 n y N6 HN61 SAH sing 323 n n N6 HN62 SAH sing 324 n n N1 C2 SAH sing 325 n y C2 N3 SAH doub 326 n y C2 H2 SAH sing 327 n n N3 C4 SAH sing 328 n y # _atom_sites.entry_id 2ONY _atom_sites.fract_transf_matrix[1][1] 0.010643 _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] 0.010643 _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] 0.005318 _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 2 SAH A 1 3001 3001 SAH SAH . D 3 TMJ A 1 2001 2001 TMJ TMC . E 4 PO4 B 1 4001 4001 PO4 PO4 . F 2 SAH B 1 3002 3002 SAH SAH . G 5 HOH A 1 3002 1001 HOH HOH . G 5 HOH A 2 3003 1002 HOH HOH . G 5 HOH A 3 3004 1003 HOH HOH . G 5 HOH A 4 3005 1004 HOH HOH . G 5 HOH A 5 3006 1005 HOH HOH . G 5 HOH A 6 3007 1006 HOH HOH . G 5 HOH A 7 3008 1007 HOH HOH . G 5 HOH A 8 3009 1008 HOH HOH . G 5 HOH A 9 3010 1009 HOH HOH . G 5 HOH A 10 3011 1010 HOH HOH . G 5 HOH A 11 3012 1011 HOH HOH . G 5 HOH A 12 3013 1012 HOH HOH . G 5 HOH A 13 3014 1013 HOH HOH . G 5 HOH A 14 3015 1014 HOH HOH . G 5 HOH A 15 3016 1015 HOH HOH . G 5 HOH A 16 3017 1016 HOH HOH . G 5 HOH A 17 3018 1017 HOH HOH . G 5 HOH A 18 3019 1018 HOH HOH . G 5 HOH A 19 3020 1019 HOH HOH . G 5 HOH A 20 3021 1020 HOH HOH . G 5 HOH A 21 3022 1022 HOH HOH . G 5 HOH A 22 3023 1023 HOH HOH . G 5 HOH A 23 3024 1024 HOH HOH . G 5 HOH A 24 3025 1025 HOH HOH . G 5 HOH A 25 3026 1026 HOH HOH . G 5 HOH A 26 3027 1027 HOH HOH . G 5 HOH A 27 3028 1031 HOH HOH . G 5 HOH A 28 3029 1044 HOH HOH . G 5 HOH A 29 3030 1065 HOH HOH . G 5 HOH A 30 3031 1066 HOH HOH . G 5 HOH A 31 3032 1068 HOH HOH . G 5 HOH A 32 3033 1073 HOH HOH . G 5 HOH A 33 3034 1074 HOH HOH . G 5 HOH A 34 3035 1077 HOH HOH . G 5 HOH A 35 3036 1082 HOH HOH . G 5 HOH A 36 3037 1084 HOH HOH . G 5 HOH A 37 3038 1085 HOH HOH . G 5 HOH A 38 3039 1086 HOH HOH . G 5 HOH A 39 3040 1087 HOH HOH . G 5 HOH A 40 3041 1088 HOH HOH . G 5 HOH A 41 3042 1089 HOH HOH . G 5 HOH A 42 3043 1090 HOH HOH . G 5 HOH A 43 3044 1091 HOH HOH . G 5 HOH A 44 3045 1092 HOH HOH . G 5 HOH A 45 3046 1094 HOH HOH . G 5 HOH A 46 3047 1095 HOH HOH . G 5 HOH A 47 3048 1096 HOH HOH . G 5 HOH A 48 3049 1097 HOH HOH . G 5 HOH A 49 3050 1098 HOH HOH . G 5 HOH A 50 3051 1099 HOH HOH . G 5 HOH A 51 3052 1100 HOH HOH . G 5 HOH A 52 3053 1101 HOH HOH . G 5 HOH A 53 3054 1115 HOH HOH . G 5 HOH A 54 3055 1121 HOH HOH . G 5 HOH A 55 3056 1122 HOH HOH . G 5 HOH A 56 3057 1127 HOH HOH . G 5 HOH A 57 3058 1128 HOH HOH . G 5 HOH A 58 3059 1139 HOH HOH . G 5 HOH A 59 3060 1141 HOH HOH . G 5 HOH A 60 3061 1142 HOH HOH . G 5 HOH A 61 3062 1143 HOH HOH . G 5 HOH A 62 3063 1144 HOH HOH . G 5 HOH A 63 3064 1145 HOH HOH . G 5 HOH A 64 3065 1146 HOH HOH . G 5 HOH A 65 3066 1147 HOH HOH . G 5 HOH A 66 3067 1148 HOH HOH . G 5 HOH A 67 3068 1149 HOH HOH . G 5 HOH A 68 3069 1150 HOH HOH . G 5 HOH A 69 3070 1151 HOH HOH . G 5 HOH A 70 3071 1152 HOH HOH . G 5 HOH A 71 3072 1153 HOH HOH . G 5 HOH A 72 3073 1154 HOH HOH . G 5 HOH A 73 3074 1155 HOH HOH . G 5 HOH A 74 3075 1156 HOH HOH . H 5 HOH B 1 4002 1021 HOH HOH . H 5 HOH B 2 4003 1028 HOH HOH . H 5 HOH B 3 4004 1029 HOH HOH . H 5 HOH B 4 4005 1030 HOH HOH . H 5 HOH B 5 4006 1032 HOH HOH . H 5 HOH B 6 4007 1033 HOH HOH . H 5 HOH B 7 4008 1034 HOH HOH . H 5 HOH B 8 4009 1035 HOH HOH . H 5 HOH B 9 4010 1036 HOH HOH . H 5 HOH B 10 4011 1037 HOH HOH . H 5 HOH B 11 4012 1038 HOH HOH . H 5 HOH B 12 4013 1039 HOH HOH . H 5 HOH B 13 4014 1040 HOH HOH . H 5 HOH B 14 4015 1041 HOH HOH . H 5 HOH B 15 4016 1042 HOH HOH . H 5 HOH B 16 4017 1043 HOH HOH . H 5 HOH B 17 4018 1045 HOH HOH . H 5 HOH B 18 4019 1046 HOH HOH . H 5 HOH B 19 4020 1047 HOH HOH . H 5 HOH B 20 4021 1048 HOH HOH . H 5 HOH B 21 4022 1049 HOH HOH . H 5 HOH B 22 4023 1050 HOH HOH . H 5 HOH B 23 4024 1051 HOH HOH . H 5 HOH B 24 4025 1052 HOH HOH . H 5 HOH B 25 4026 1053 HOH HOH . H 5 HOH B 26 4027 1054 HOH HOH . H 5 HOH B 27 4028 1055 HOH HOH . H 5 HOH B 28 4029 1056 HOH HOH . H 5 HOH B 29 4030 1057 HOH HOH . H 5 HOH B 30 4031 1058 HOH HOH . H 5 HOH B 31 4032 1059 HOH HOH . H 5 HOH B 32 4033 1060 HOH HOH . H 5 HOH B 33 4034 1061 HOH HOH . H 5 HOH B 34 4035 1062 HOH HOH . H 5 HOH B 35 4036 1063 HOH HOH . H 5 HOH B 36 4037 1064 HOH HOH . H 5 HOH B 37 4038 1067 HOH HOH . H 5 HOH B 38 4039 1069 HOH HOH . H 5 HOH B 39 4040 1070 HOH HOH . H 5 HOH B 40 4041 1071 HOH HOH . H 5 HOH B 41 4042 1072 HOH HOH . H 5 HOH B 42 4043 1075 HOH HOH . H 5 HOH B 43 4044 1076 HOH HOH . H 5 HOH B 44 4045 1078 HOH HOH . H 5 HOH B 45 4046 1079 HOH HOH . H 5 HOH B 46 4047 1080 HOH HOH . H 5 HOH B 47 4048 1081 HOH HOH . H 5 HOH B 48 4049 1083 HOH HOH . H 5 HOH B 49 4050 1093 HOH HOH . H 5 HOH B 50 4051 1102 HOH HOH . H 5 HOH B 51 4052 1103 HOH HOH . H 5 HOH B 52 4053 1104 HOH HOH . H 5 HOH B 53 4054 1105 HOH HOH . H 5 HOH B 54 4055 1106 HOH HOH . H 5 HOH B 55 4056 1107 HOH HOH . H 5 HOH B 56 4057 1108 HOH HOH . H 5 HOH B 57 4058 1109 HOH HOH . H 5 HOH B 58 4059 1110 HOH HOH . H 5 HOH B 59 4060 1111 HOH HOH . H 5 HOH B 60 4061 1112 HOH HOH . H 5 HOH B 61 4062 1113 HOH HOH . H 5 HOH B 62 4063 1114 HOH HOH . H 5 HOH B 63 4064 1116 HOH HOH . H 5 HOH B 64 4065 1117 HOH HOH . H 5 HOH B 65 4066 1118 HOH HOH . H 5 HOH B 66 4067 1119 HOH HOH . H 5 HOH B 67 4068 1120 HOH HOH . H 5 HOH B 68 4069 1123 HOH HOH . H 5 HOH B 69 4070 1124 HOH HOH . H 5 HOH B 70 4071 1125 HOH HOH . H 5 HOH B 71 4072 1126 HOH HOH . H 5 HOH B 72 4073 1129 HOH HOH . H 5 HOH B 73 4074 1130 HOH HOH . H 5 HOH B 74 4075 1131 HOH HOH . H 5 HOH B 75 4076 1132 HOH HOH . H 5 HOH B 76 4077 1133 HOH HOH . H 5 HOH B 77 4078 1134 HOH HOH . H 5 HOH B 78 4079 1135 HOH HOH . H 5 HOH B 79 4080 1136 HOH HOH . H 5 HOH B 80 4081 1137 HOH HOH . H 5 HOH B 81 4082 1138 HOH HOH . H 5 HOH B 82 4083 1140 HOH HOH . H 5 HOH B 83 4084 1157 HOH HOH . H 5 HOH B 84 4085 1158 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 N SAH . . . F 2 27.992 50.913 -27.567 1 53.12 ? N SAH 3002 B 1 HETATM 2 C CA SAH . . . F 2 28.846 51.879 -26.891 1 52.8 ? CA SAH 3002 B 1 HETATM 3 C CB SAH . . . F 2 29.769 52.601 -27.905 1 55.98 ? CB SAH 3002 B 1 HETATM 4 C CG SAH . . . F 2 29.112 53.345 -29.111 1 56.25 ? CG SAH 3002 B 1 HETATM 5 S SD SAH . . . F 2 30.376 54.255 -30.111 1 58.8 ? SD SAH 3002 B 1 HETATM 6 C C SAH . . . F 2 28.012 52.863 -26.086 1 54.36 ? C SAH 3002 B 1 HETATM 7 O O SAH . . . F 2 26.8 52.594 -25.926 1 54.03 ? O SAH 3002 B 1 HETATM 8 O OXT SAH . . . F 2 28.573 53.875 -25.605 1 54.63 ? OXT SAH 3002 B 1 HETATM 9 C C5' SAH . . . F 2 30.279 53.553 -31.773 1 53.94 ? C5' SAH 3002 B 1 HETATM 10 C C4' SAH . . . F 2 31.059 52.266 -31.879 1 58.01 ? C4' SAH 3002 B 1 HETATM 11 O O4' SAH . . . F 2 30.883 51.636 -33.177 1 57.92 ? O4' SAH 3002 B 1 HETATM 12 C C3' SAH . . . F 2 32.564 52.3 -31.607 1 58.62 ? C3' SAH 3002 B 1 HETATM 13 O O3' SAH . . . F 2 32.908 51.394 -30.564 1 58.36 ? O3' SAH 3002 B 1 HETATM 14 C C2' SAH . . . F 2 33.175 51.893 -32.947 1 59.98 ? C2' SAH 3002 B 1 HETATM 15 O O2' SAH . . . F 2 34.388 51.173 -32.851 1 62.64 ? O2' SAH 3002 B 1 HETATM 16 C C1' SAH . . . F 2 32.083 51 -33.528 1 58.2 ? C1' SAH 3002 B 1 HETATM 17 N N9 SAH . . . F 2 32.139 50.845 -34.98 1 58.22 ? N9 SAH 3002 B 1 HETATM 18 C C8 SAH . . . F 2 32.837 51.643 -35.935 1 58.24 ? C8 SAH 3002 B 1 HETATM 19 N N7 SAH . . . F 2 32.742 51.187 -37.159 1 60.02 ? N7 SAH 3002 B 1 HETATM 20 C C5 SAH . . . F 2 31.944 50.062 -37.018 1 61.47 ? C5 SAH 3002 B 1 HETATM 21 C C6 SAH . . . F 2 31.509 49.153 -38.004 1 62.2 ? C6 SAH 3002 B 1 HETATM 22 N N6 SAH . . . F 2 31.833 49.247 -39.296 1 62.37 ? N6 SAH 3002 B 1 HETATM 23 N N1 SAH . . . F 2 30.714 48.122 -37.599 1 61.92 ? N1 SAH 3002 B 1 HETATM 24 C C2 SAH . . . F 2 30.396 48.032 -36.284 1 60.86 ? C2 SAH 3002 B 1 HETATM 25 N N3 SAH . . . F 2 30.765 48.84 -35.266 1 61 ? N3 SAH 3002 B 1 HETATM 26 C C4 SAH . . . F 2 31.549 49.846 -35.707 1 60.24 ? C4 SAH 3002 B 1 # _model_server_stats.io_time_ms 8 _model_server_stats.parse_time_ms 8 _model_server_stats.create_model_time_ms 15 _model_server_stats.query_time_ms 316 _model_server_stats.encode_time_ms 2 _model_server_stats.element_count 26 #