data_3SYU # _model_server_result.job_id mwjLLvBT8IAHNAIM6csJcA _model_server_result.datetime_utc '2024-11-29 17:32:11' _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 3syu # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"D","auth_seq_id":105}' # _entry.id 3SYU # _exptl.entry_id 3SYU _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 363.221 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-2'-MONOPHOSPHATE" _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 3SYU _cell.length_a 88.69 _cell.length_b 88.69 _cell.length_c 88.69 _cell.Z_PDB 24 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3SYU _symmetry.cell_setting ? _symmetry.Int_Tables_number 197 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'I 2 3' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _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,F _pdbx_struct_assembly_gen.assembly_id 1 _pdbx_struct_assembly_gen.oper_expression 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 # _struct_asym.details ? _struct_asym.entity_id 3 _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 disulf ? disulf1 A SG CYS 2 A CYS 2 1_555 A SG CYS 10 A CYS 10 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? disulf ? disulf2 A SG CYS 6 A CYS 6 1_555 A SG CYS 103 A CYS 103 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.028 ? covale ? covale1 A C TYR 57 A TYR 57 1_555 A N CGA 58 A CGA 58 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.314 ? covale ? covale2 A C CGA 58 A CGA 58 1_555 A N TRP 59 A TRP 59 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 1.324 ? metalc ? metalc1 A O GLY 30 A GLY 30 1_555 B NA NA . A NA 106 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.397 ? metalc ? metalc2 B NA NA . A NA 106 1_555 F O HOH . A HOH 236 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.233 ? metalc ? metalc3 B NA NA . A NA 106 1_555 F O HOH . A HOH 992 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.549 ? metalc ? metalc4 C NA NA . A NA 107 1_555 F O HOH . A HOH 268 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.392 ? # _chem_comp.formula 'C10 H14 N5 O8 P' _chem_comp.formula_weight 363.221 _chem_comp.id 2GP _chem_comp.mon_nstd_flag . _chem_comp.name "GUANOSINE-2'-MONOPHOSPHATE" _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 P O1P 2GP doub 1 n n P O2P 2GP sing 2 n n P O3P 2GP sing 3 n n P O2' 2GP sing 4 n n O2P HOP2 2GP sing 5 n n O3P HOP3 2GP sing 6 n n O5' C5' 2GP sing 7 n n O5' HO5' 2GP sing 8 n n C5' C4' 2GP sing 9 n n C5' "H5'1" 2GP sing 10 n n C5' "H5'2" 2GP sing 11 n n C4' O4' 2GP sing 12 n n C4' C3' 2GP sing 13 n n C4' H4' 2GP sing 14 n n O4' C1' 2GP sing 15 n n C3' O3' 2GP sing 16 n n C3' C2' 2GP sing 17 n n C3' H3' 2GP sing 18 n n O3' HO3' 2GP sing 19 n n C2' O2' 2GP sing 20 n n C2' C1' 2GP sing 21 n n C2' H2' 2GP sing 22 n n C1' N9 2GP sing 23 n n C1' H1' 2GP sing 24 n n N9 C8 2GP sing 25 n y N9 C4 2GP sing 26 n y C8 N7 2GP doub 27 n y C8 H8 2GP sing 28 n n N7 C5 2GP sing 29 n y C5 C6 2GP sing 30 n n C5 C4 2GP doub 31 n y C6 O6 2GP doub 32 n n C6 N1 2GP sing 33 n n N1 C2 2GP sing 34 n n N1 HN1 2GP sing 35 n n C2 N2 2GP sing 36 n n C2 N3 2GP doub 37 n n N2 HN21 2GP sing 38 n n N2 HN22 2GP sing 39 n n N3 C4 2GP sing 40 n n # _atom_sites.entry_id 3SYU _atom_sites.fract_transf_matrix[1][1] 0.011275 _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] 0.011275 _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] 0.011275 _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 NA A 1 106 106 NA NA . C 2 NA A 1 107 107 NA NA . D 3 2GP A 1 105 105 2GP 2GP . E 4 UNX A 1 991 991 UNX UNX . F 5 HOH A 1 201 201 HOH HOH . F 5 HOH A 2 202 202 HOH HOH . F 5 HOH A 3 203 203 HOH HOH . F 5 HOH A 4 204 204 HOH HOH . F 5 HOH A 5 205 205 HOH HOH . F 5 HOH A 6 206 206 HOH HOH . F 5 HOH A 7 207 207 HOH HOH . F 5 HOH A 8 208 208 HOH HOH . F 5 HOH A 9 209 209 HOH HOH . F 5 HOH A 10 210 210 HOH HOH . F 5 HOH A 11 212 212 HOH HOH . F 5 HOH A 12 213 213 HOH HOH . F 5 HOH A 13 215 215 HOH HOH . F 5 HOH A 14 216 216 HOH HOH . F 5 HOH A 15 217 217 HOH HOH . F 5 HOH A 16 218 218 HOH HOH . F 5 HOH A 17 219 219 HOH HOH . F 5 HOH A 18 220 220 HOH HOH . F 5 HOH A 19 222 222 HOH HOH . F 5 HOH A 20 223 223 HOH HOH . F 5 HOH A 21 224 224 HOH HOH . F 5 HOH A 22 226 226 HOH HOH . F 5 HOH A 23 231 231 HOH HOH . F 5 HOH A 24 232 232 HOH HOH . F 5 HOH A 25 233 233 HOH HOH . F 5 HOH A 26 234 234 HOH HOH . F 5 HOH A 27 236 236 HOH HOH . F 5 HOH A 28 239 239 HOH HOH . F 5 HOH A 29 242 242 HOH HOH . F 5 HOH A 30 243 243 HOH HOH . F 5 HOH A 31 251 251 HOH HOH . F 5 HOH A 32 252 252 HOH HOH . F 5 HOH A 33 256 256 HOH HOH . F 5 HOH A 34 258 258 HOH HOH . F 5 HOH A 35 259 259 HOH HOH . F 5 HOH A 36 260 260 HOH HOH . F 5 HOH A 37 261 261 HOH HOH . F 5 HOH A 38 263 263 HOH HOH . F 5 HOH A 39 267 267 HOH HOH . F 5 HOH A 40 268 268 HOH HOH . F 5 HOH A 41 269 269 HOH HOH . F 5 HOH A 42 271 271 HOH HOH . F 5 HOH A 43 992 992 HOH HOH . F 5 HOH A 44 993 993 HOH HOH . F 5 HOH A 45 994 994 HOH HOH . F 5 HOH A 46 996 996 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 P P 2GP . . . D 3 22.841 -48.01 -0.245 0.89 33.51 ? P 2GP 105 A 1 HETATM 2 O O1P 2GP . . . D 3 24.061 -47.811 -1.038 0.89 32.9 ? O1P 2GP 105 A 1 HETATM 3 O O2P 2GP . . . D 3 21.538 -47.428 -0.882 0.89 39.44 ? O2P 2GP 105 A 1 HETATM 4 O O3P 2GP . . . D 3 22.531 -49.443 0.162 0.89 36.15 ? O3P 2GP 105 A 1 HETATM 5 O O5' 2GP . . . D 3 19.438 -47.966 3.778 0.89 40.46 ? O5' 2GP 105 A 1 HETATM 6 C C5' 2GP . . . D 3 19.591 -46.666 4.322 0.89 36.95 ? C5' 2GP 105 A 1 HETATM 7 C C4' 2GP . . . D 3 20.793 -45.96 3.742 0.89 32.84 ? C4' 2GP 105 A 1 HETATM 8 O O4' 2GP . . . D 3 21.999 -46.416 4.413 0.89 30 ? O4' 2GP 105 A 1 HETATM 9 C C3' 2GP . . . D 3 21.019 -46.193 2.249 0.89 37.57 ? C3' 2GP 105 A 1 HETATM 10 O O3' 2GP . . . D 3 21.455 -44.992 1.62 0.89 40.78 ? O3' 2GP 105 A 1 HETATM 11 C C2' 2GP . . . D 3 22.136 -47.233 2.242 0.89 34.42 ? C2' 2GP 105 A 1 HETATM 12 O O2' 2GP . . . D 3 22.978 -47.131 1.079 0.89 29.77 ? O2' 2GP 105 A 1 HETATM 13 C C1' 2GP . . . D 3 22.956 -46.785 3.441 0.89 29.32 ? C1' 2GP 105 A 1 HETATM 14 N N9 2GP . . . D 3 23.814 -47.848 4.012 0.89 26.09 ? N9 2GP 105 A 1 HETATM 15 C C8 2GP . . . D 3 23.437 -49.097 4.436 0.89 24.65 ? C8 2GP 105 A 1 HETATM 16 N N7 2GP . . . D 3 24.439 -49.854 4.81 0.89 25.15 ? N7 2GP 105 A 1 HETATM 17 C C5 2GP . . . D 3 25.553 -49.061 4.593 0.89 23.17 ? C5 2GP 105 A 1 HETATM 18 C C6 2GP . . . D 3 26.937 -49.33 4.746 0.89 24.34 ? C6 2GP 105 A 1 HETATM 19 O O6 2GP . . . D 3 27.459 -50.4 5.074 0.89 24.05 ? O6 2GP 105 A 1 HETATM 20 N N1 2GP . . . D 3 27.719 -48.226 4.445 0.89 25.75 ? N1 2GP 105 A 1 HETATM 21 C C2 2GP . . . D 3 27.25 -47.002 4.019 0.89 23.63 ? C2 2GP 105 A 1 HETATM 22 N N2 2GP . . . D 3 28.158 -46.054 3.775 0.89 25.04 ? N2 2GP 105 A 1 HETATM 23 N N3 2GP . . . D 3 25.959 -46.737 3.843 0.89 22.57 ? N3 2GP 105 A 1 HETATM 24 C C4 2GP . . . D 3 25.17 -47.799 4.135 0.89 23.71 ? C4 2GP 105 A 1 HETATM 25 H HOP3 2GP . . . D 3 21.658 -49.769 0.509 0.89 35.71 ? HOP3 2GP 105 A 1 HETATM 26 H HO5' 2GP . . . D 3 20.221 -48.492 4.09 0.89 40.05 ? HO5' 2GP 105 A 1 HETATM 27 H "H5'1" 2GP . . . D 3 19.73 -46.751 5.398 0.89 36.32 ? "H5'1" 2GP 105 A 1 HETATM 28 H "H5'2" 2GP . . . D 3 18.683 -46.084 4.173 0.89 37.87 ? "H5'2" 2GP 105 A 1 HETATM 29 H H4' 2GP . . . D 3 20.731 -44.895 3.961 0.89 31.65 ? H4' 2GP 105 A 1 HETATM 30 H H3' 2GP . . . D 3 20.139 -46.579 1.737 0.89 37.73 ? H3' 2GP 105 A 1 HETATM 31 H HO3' 2GP . . . D 3 21.821 -45.259 0.736 0.89 41.3 ? HO3' 2GP 105 A 1 HETATM 32 H H2' 2GP . . . D 3 21.738 -48.243 2.327 0.89 35.52 ? H2' 2GP 105 A 1 HETATM 33 H H1' 2GP . . . D 3 23.577 -45.93 3.179 0.89 28.29 ? H1' 2GP 105 A 1 HETATM 34 H H8 2GP . . . D 3 22.4 -49.427 4.454 0.89 26.29 ? H8 2GP 105 A 1 HETATM 35 H HN1 2GP . . . D 3 28.711 -48.379 4.586 0.89 25.99 ? HN1 2GP 105 A 1 HETATM 36 H HN21 2GP . . . D 3 29.145 -46.224 3.937 0.89 24.47 ? HN21 2GP 105 A 1 HETATM 37 H HN22 2GP . . . D 3 27.933 -45.151 3.371 0.89 25.99 ? HN22 2GP 105 A 1 # _model_server_stats.io_time_ms 9 _model_server_stats.parse_time_ms 25 _model_server_stats.create_model_time_ms 7 _model_server_stats.query_time_ms 329 _model_server_stats.encode_time_ms 10 _model_server_stats.element_count 37 #