data_3BB3 # _model_server_result.job_id 5tFrDSa8ObPbK3zug-NfWg _model_server_result.datetime_utc '2025-03-09 04:47:37' _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 3bb3 # _model_server_params.name atom_site _model_server_params.value '{"label_asym_id":"C","auth_seq_id":281}' # _entry.id 3BB3 # _exptl.entry_id 3BB3 _exptl.method 'X-RAY DIFFRACTION' # _entity.details ? _entity.formula_weight 443.201 _entity.id 3 _entity.src_method syn _entity.type non-polymer _entity.pdbx_description "GUANOSINE-5'-DIPHOSPHATE" _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 3BB3 _cell.length_a 121.617 _cell.length_b 121.617 _cell.length_c 42.769 _cell.Z_PDB 8 _cell.pdbx_unique_axis ? # _symmetry.entry_id 3BB3 _symmetry.cell_setting ? _symmetry.Int_Tables_number 92 _symmetry.space_group_name_Hall ? _symmetry.space_group_name_H-M 'P 41 21 2' # _pdbx_struct_assembly.method_details PISA _pdbx_struct_assembly.oligomeric_details monomeric _pdbx_struct_assembly.oligomeric_count 1 _pdbx_struct_assembly.details 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 # _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 C _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 metalc ? metalc1 A OG SER 50 A SER 50 1_555 B MG MG . A MG 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.174 ? metalc ? metalc2 C O3B GDP . A GDP 281 1_555 B MG MG . A MG 282 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.077 ? metalc ? metalc3 B MG MG . A MG 282 1_555 D O HOH . A HOH 283 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.079 ? metalc ? metalc4 B MG MG . A MG 282 1_555 D O HOH . A HOH 284 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.106 ? metalc ? metalc5 B MG MG . A MG 282 1_555 D O HOH . A HOH 285 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.072 ? metalc ? metalc6 B MG MG . A MG 282 1_555 D O HOH . A HOH 286 1_555 ? ? ? ? ? ? ? ? ? ? ? ? 2.071 ? # _chem_comp.formula 'C10 H15 N5 O11 P2' _chem_comp.formula_weight 443.201 _chem_comp.id GDP _chem_comp.mon_nstd_flag n _chem_comp.name "GUANOSINE-5'-DIPHOSPHATE" _chem_comp.type 'rna linking' _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 PB O1B GDP doub 83 n n PB O2B GDP sing 84 n n PB O3B GDP sing 85 n n PB O3A GDP sing 86 n n O2B HOB2 GDP sing 87 n n O3B HOB3 GDP sing 88 n n O3A PA GDP sing 89 n n PA O1A GDP doub 90 n n PA O2A GDP sing 91 n n PA O5' GDP sing 92 n n O2A HOA2 GDP sing 93 n n O5' C5' GDP sing 94 n n C5' C4' GDP sing 95 n n C5' H5' GDP sing 96 n n C5' "H5''" GDP sing 97 n n C4' O4' GDP sing 98 n n C4' C3' GDP sing 99 n n C4' H4' GDP sing 100 n n O4' C1' GDP sing 101 n n C3' O3' GDP sing 102 n n C3' C2' GDP sing 103 n n C3' H3' GDP sing 104 n n O3' HO3' GDP sing 105 n n C2' O2' GDP sing 106 n n C2' C1' GDP sing 107 n n C2' H2' GDP sing 108 n n O2' HO2' GDP sing 109 n n C1' N9 GDP sing 110 n n C1' H1' GDP sing 111 n n N9 C8 GDP sing 112 n y N9 C4 GDP sing 113 n y C8 N7 GDP doub 114 n y C8 H8 GDP sing 115 n n N7 C5 GDP sing 116 n y C5 C6 GDP sing 117 n n C5 C4 GDP doub 118 n y C6 O6 GDP doub 119 n n C6 N1 GDP sing 120 n n N1 C2 GDP sing 121 n n N1 HN1 GDP sing 122 n n C2 N2 GDP sing 123 n n C2 N3 GDP doub 124 n n N2 HN21 GDP sing 125 n n N2 HN22 GDP sing 126 n n N3 C4 GDP sing 127 n n # _atom_sites.entry_id 3BB3 _atom_sites.fract_transf_matrix[1][1] 0.008223 _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] 0.008223 _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] 0.023381 _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 1 282 282 MG MG . C 3 GDP A 1 281 281 GDP GDP . D 4 HOH A 1 283 283 HOH WAT . D 4 HOH A 2 284 284 HOH WAT . D 4 HOH A 3 285 285 HOH WAT . D 4 HOH A 4 286 286 HOH WAT . D 4 HOH A 5 287 1 HOH WAT . D 4 HOH A 6 288 2 HOH WAT . D 4 HOH A 7 289 3 HOH WAT . D 4 HOH A 8 290 4 HOH WAT . D 4 HOH A 9 291 5 HOH WAT . D 4 HOH A 10 292 6 HOH WAT . D 4 HOH A 11 293 7 HOH WAT . D 4 HOH A 12 294 8 HOH WAT . D 4 HOH A 13 295 9 HOH WAT . D 4 HOH A 14 296 10 HOH WAT . D 4 HOH A 15 297 11 HOH WAT . D 4 HOH A 16 298 12 HOH WAT . D 4 HOH A 17 299 13 HOH WAT . D 4 HOH A 18 300 14 HOH WAT . D 4 HOH A 19 301 15 HOH WAT . D 4 HOH A 20 302 16 HOH WAT . D 4 HOH A 21 303 17 HOH WAT . D 4 HOH A 22 304 18 HOH WAT . D 4 HOH A 23 305 19 HOH WAT . D 4 HOH A 24 306 20 HOH WAT . D 4 HOH A 25 307 21 HOH WAT . D 4 HOH A 26 308 22 HOH WAT . D 4 HOH A 27 309 23 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 P PB GDP . . . C 3 18.336 44.844 15.077 1 103.11 ? PB GDP 281 A 1 HETATM 2 O O1B GDP . . . C 3 17.944 45.224 13.666 1 104.81 ? O1B GDP 281 A 1 HETATM 3 O O2B GDP . . . C 3 19.145 45.897 15.812 1 104.11 ? O2B GDP 281 A 1 HETATM 4 O O3B GDP . . . C 3 18.949 43.342 15.059 1 103.62 ? O3B GDP 281 A 1 HETATM 5 O O3A GDP . . . C 3 16.967 44.512 15.881 1 99.91 ? O3A GDP 281 A 1 HETATM 6 P PA GDP . . . C 3 16.762 43.698 17.265 1 93.62 ? PA GDP 281 A 1 HETATM 7 O O1A GDP . . . C 3 18.094 43.6 17.93 1 95.72 ? O1A GDP 281 A 1 HETATM 8 O O2A GDP . . . C 3 15.966 42.466 16.961 1 93.18 ? O2A GDP 281 A 1 HETATM 9 O O5' GDP . . . C 3 15.789 44.602 18.175 1 93.43 ? O5' GDP 281 A 1 HETATM 10 C C5' GDP . . . C 3 15.852 45.985 18.578 1 94.67 ? C5' GDP 281 A 1 HETATM 11 C C4' GDP . . . C 3 14.801 46.182 19.706 1 96.92 ? C4' GDP 281 A 1 HETATM 12 O O4' GDP . . . C 3 13.466 46.225 19.168 1 98.61 ? O4' GDP 281 A 1 HETATM 13 C C3' GDP . . . C 3 14.731 45.054 20.753 1 97.73 ? C3' GDP 281 A 1 HETATM 14 O O3' GDP . . . C 3 14.736 45.553 22.106 1 98.56 ? O3' GDP 281 A 1 HETATM 15 C C2' GDP . . . C 3 13.498 44.212 20.36 1 97.27 ? C2' GDP 281 A 1 HETATM 16 O O2' GDP . . . C 3 12.789 43.495 21.375 1 98.85 ? O2' GDP 281 A 1 HETATM 17 C C1' GDP . . . C 3 12.585 45.197 19.684 1 95.81 ? C1' GDP 281 A 1 HETATM 18 N N9 GDP . . . C 3 11.799 44.564 18.579 1 95.42 ? N9 GDP 281 A 1 HETATM 19 C C8 GDP . . . C 3 12.281 43.92 17.479 1 94.52 ? C8 GDP 281 A 1 HETATM 20 N N7 GDP . . . C 3 11.266 43.499 16.695 1 93.11 ? N7 GDP 281 A 1 HETATM 21 C C5 GDP . . . C 3 10.125 43.907 17.318 1 94.01 ? C5 GDP 281 A 1 HETATM 22 C C6 GDP . . . C 3 8.662 43.78 17.007 1 94.31 ? C6 GDP 281 A 1 HETATM 23 O O6 GDP . . . C 3 8.217 43.22 15.976 1 93.78 ? O6 GDP 281 A 1 HETATM 24 N N1 GDP . . . C 3 7.791 44.306 17.902 1 95.04 ? N1 GDP 281 A 1 HETATM 25 C C2 GDP . . . C 3 8.198 44.934 19.027 1 94.02 ? C2 GDP 281 A 1 HETATM 26 N N2 GDP . . . C 3 7.227 45.403 19.813 1 93.89 ? N2 GDP 281 A 1 HETATM 27 N N3 GDP . . . C 3 9.512 45.087 19.338 1 93.84 ? N3 GDP 281 A 1 HETATM 28 C C4 GDP . . . C 3 10.468 44.577 18.504 1 94.05 ? C4 GDP 281 A 1 # _model_server_stats.io_time_ms 7 _model_server_stats.parse_time_ms 9 _model_server_stats.create_model_time_ms 3 _model_server_stats.query_time_ms 307 _model_server_stats.encode_time_ms 4 _model_server_stats.element_count 28 #